diff --git a/babs/babs.py b/babs/babs.py
index c52fa2d1..78024e0a 100644
--- a/babs/babs.py
+++ b/babs/babs.py
@@ -25,6 +25,7 @@
                         generate_cmd_set_envvar,
                         generate_cmd_filterfile,
                         generate_cmd_singularityRun_from_config, generate_cmd_unzip_inputds,
+                        get_info_zip_foldernames,
                         generate_cmd_zipping_from_config,
                         validate_type_session,
                         validate_type_system,
@@ -2257,10 +2258,9 @@ def generate_bash_run_bidsapp(self, bash_path, input_ds, type_session):
         When writing `singularity run` part, each chunk to write should start with " \\" + "\n\t",
         meaning, starting with space, a backward slash, a return, and a tab.
         """
-        from .constants import PATH_FS_LICENSE_IN_CONTAINER
+        from .constants import PATH_FS_LICENSE_IN_CONTAINER, OUTPUT_MAIN_FOLDERNAME
 
         type_session = validate_type_session(type_session)
-        output_foldername = "outputs"    # folername of BIDS App outputs
 
         # Check if the folder exist; if not, create it:
         bash_dir = op.dirname(bash_path)
@@ -2268,6 +2268,7 @@ def generate_bash_run_bidsapp(self, bash_path, input_ds, type_session):
             os.makedirs(bash_dir)
 
         # check if `self.config` from the YAML file contains information we need:
+        # 1. check `singularity_run` section:
         if "singularity_run" not in self.config:
             # sanity check: there should be only one input ds
             #   otherwise need to specify in this section:
@@ -2295,10 +2296,14 @@ def generate_bash_run_bidsapp(self, bash_path, input_ds, type_session):
             cmd_singularity_flags, flag_fs_license, path_fs_license, singuRun_input_dir = \
                 generate_cmd_singularityRun_from_config(self.config, input_ds)
 
-        print()
-
         # TODO: also corporate the `call-fmt` in `datalad containers-add`
 
+        # 2. check `zip_foldernames` section:
+        dict_zip_foldernames, if_mk_output_folder, path_output_folder = \
+            get_info_zip_foldernames(self.config)
+
+        print()
+
         # Check if the bash file already exist:
         if op.exists(bash_path):
             os.remove(bash_path)  # remove it
@@ -2386,7 +2391,7 @@ def generate_bash_run_bidsapp(self, bash_path, input_ds, type_session):
         cmd_head_singularityRun += " \\" + "\n\t"
         cmd_head_singularityRun += singuRun_input_dir  # inputs/data/<name>
         cmd_head_singularityRun += " \\" + "\n\t"
-        cmd_head_singularityRun += output_foldername   # output folder
+        cmd_head_singularityRun += path_output_folder    # defined above
 
         # currently all BIDS App support `participant` positional argu:
         cmd_head_singularityRun += " \\" + "\n\t"
@@ -2411,7 +2416,7 @@ def generate_bash_run_bidsapp(self, bash_path, input_ds, type_session):
         print(cmd_head_singularityRun + cmd_singularity_flags)
 
         # Zip:
-        cmd_zip = generate_cmd_zipping_from_config(self.config, type_session, output_foldername)
+        cmd_zip = generate_cmd_zipping_from_config(dict_zip_foldernames, type_session)
         bash_file.write(cmd_zip)
 
         # Delete folders and files:
@@ -2419,7 +2424,8 @@ def generate_bash_run_bidsapp(self, bash_path, input_ds, type_session):
         rm -rf prep .git/tmp/wkdir
         rm ${filterfile}
         """
-        cmd_clean = "rm -rf " + output_foldername + " " + ".git/tmp/wkdir" + "\n"
+        cmd_clean = "rm -rf " + OUTPUT_MAIN_FOLDERNAME + " " + ".git/tmp/wkdir" + "\n"
+        # ^^ rm the entire output folder `outputs`
         if flag_filterfile is True:
             cmd_clean += "rm ${filterfile}" + " \n"
 
diff --git a/babs/constants.py b/babs/constants.py
index 451ab9f6..dfb1c6b8 100644
--- a/babs/constants.py
+++ b/babs/constants.py
@@ -1,3 +1,8 @@
 MSG_NO_ALERT_IN_LOGS = "BABS: No alert message found in log files."
 CHECK_MARK = u'\N{check mark}'  # can be used by print(CHECK_MARK)
 PATH_FS_LICENSE_IN_CONTAINER = "/SGLR/FREESURFER_HOME/license.txt"
+
+# The upper layer of output folder - BABS expects there are sub-folers in it to zip:
+OUTPUT_MAIN_FOLDERNAME = "outputs"
+# Placeholder for creating a sub-folder to hold all outputs:
+PLACEHOLDER_MK_SUB_OUTPUT_FOLDER = "$TO_CREATE_FOLDER"
diff --git a/babs/utils.py b/babs/utils.py
index b8f3ba2b..f53794a3 100644
--- a/babs/utils.py
+++ b/babs/utils.py
@@ -442,20 +442,105 @@ def generate_cmd_set_envvar(env_var_name):
 
     return cmd, env_var_value, env_var_value_in_container
 
-
-def generate_cmd_zipping_from_config(config, type_session, output_foldername="outputs"):
+def get_info_zip_foldernames(config):
     """
-    This is to generate bash command to zip BIDS App outputs.
+    This is to get information from `zip_foldernames` section
+    in the container configuration YAML file.
+    Note that users have option to request creating a sub-folder in `outputs` folder,
+    if the BIDS App does not do so (e.g., fMRIPrep new BIDS output layout).
+
+    Information:
+    1. foldernames to zip
+    2. whether the user requests creating a sub-folder
+    3. path to the output dir to be used in the `singularity run`
 
     Parameters:
     ------------
     config: dictionary
         attribute `config` in class Container;
         got from `read_container_config_yaml()`
+
+    Returns:
+    ---------
+    dict_zip_foldernames: dict
+        `config["zip_foldernames"]` w/ placeholder key/value pair removed.
+    if_mk_folder: bool
+        whether requested to create a sub-folder in `outputs`.
+    path_output_folder: str
+        output folder used in `singularity run` of the BIDS App.
+        see examples below.
+
+    Examples `path_output_folder` of BIDS App:
+    -------------------------------------------------
+    In `zip_foldernames` section:
+    1. No placeholder:                  outputs
+    2. placeholder = true & 1 folder:   outputs/<foldername>
+
+    Notes:
+    ----------
+    In fact, we use `OUTPUT_MAIN_FOLDERNAME` to define the 'outputs' string.
+    """
+
+    from .constants import OUTPUT_MAIN_FOLDERNAME, PLACEHOLDER_MK_SUB_OUTPUT_FOLDER
+
+    # Sanity check: this section should exist:
+    if "zip_foldernames" not in config:
+        raise Exception("The `container_config_yaml_file` does not contain"
+                        + " the section `zip_foldernames`. Please add this section!")
+
+    # Check if placeholder to make a sub-folder in `outputs` folder:
+    if_mk_folder = False
+    if PLACEHOLDER_MK_SUB_OUTPUT_FOLDER in config["zip_foldernames"]:
+        # check its value:
+        #   there cannot be two placeholders (w/ same strings);
+        #   otherwise error when loading yaml file
+        value = config["zip_foldernames"][PLACEHOLDER_MK_SUB_OUTPUT_FOLDER]
+        if value.lower() == "true":    # lower case is "true"
+            if_mk_folder = True
+
+    # Get the dict of foldernames + version number:
+    dict_zip_foldernames = config["zip_foldernames"]
+    if if_mk_folder:
+        # remove key of placeholder if there is:
+        _ = dict_zip_foldernames.pop(PLACEHOLDER_MK_SUB_OUTPUT_FOLDER)
+        # ^^ the returned value is the value of this key
+
+        # sanity check: if there was placeholder, we expect only one output folder to create:
+        if len(dict_zip_foldernames) == 1:   # good
+            pass
+        elif len(dict_zip_foldernames) == 0:  # only placeholder was provided:
+            raise Exception("Only placeholder '" + PLACEHOLDER_MK_SUB_OUTPUT_FOLDER + "'"
+                            + " is provided in section 'zip_foldernames'."
+                            + " You should also provide"
+                            + " a name of output folder to create and zip.")
+        else:   # len(dict_zip_foldernames) > 1:   # more than one foldernames provided:
+            raise Exception("You ask BABS to create more than one output folder,"
+                            + " but BABS can only create one output folder."
+                            + " Please only keep one of them in 'zip_foldernames' section.")
+
+    # Get the list of foldernames (w/o version number):
+    list_foldernames = list(dict_zip_foldernames.keys())
+
+    # Generate the output folder path:
+    path_output_folder = OUTPUT_MAIN_FOLDERNAME
+    if if_mk_folder:
+        the_folder = list_foldernames[0]   # there is only one folder
+        path_output_folder += "/" + the_folder
+
+    return dict_zip_foldernames, if_mk_folder, path_output_folder
+
+
+def generate_cmd_zipping_from_config(dict_zip_foldernames, type_session):
+    """
+    This is to generate bash command to zip BIDS App outputs.
+
+    Parameters:
+    ------------
+    dict_zip_foldernames: dictionary
+        `config["zip_foldernames"]` w/ placeholder key/value pair removed.
+        got from `get_info_zip_foldernames()`.
     type_session: str
         "multi-ses" or "single-ses"
-    output_foldername: str
-        the foldername of the outputs of BIDS App; default is "outputs".
 
     Returns:
     ---------
@@ -464,8 +549,10 @@ def generate_cmd_zipping_from_config(config, type_session, output_foldername="ou
         based on section `zip_foldernames` in the yaml file.
     """
 
+    from .constants import OUTPUT_MAIN_FOLDERNAME
+
     # cd to output folder:
-    cmd = "cd " + output_foldername + "\n"
+    cmd = "cd " + OUTPUT_MAIN_FOLDERNAME + "\n"
 
     # 7z:
     if type_session == "multi-ses":
@@ -473,28 +560,23 @@ def generate_cmd_zipping_from_config(config, type_session, output_foldername="ou
     else:
         str_sesid = ""
 
-    if "zip_foldernames" in config:
-        value_temp = ""
-        temp = 0
-
-        for key, value in config["zip_foldernames"].items():
-            # each key is a foldername to be zipped;
-            # each value is the version string;
-            temp = temp + 1
-            if (temp != 1) & (value_temp != value):    # not matching last value
-                warnings.warn("In section `zip_foldernames` in `container_config_yaml_file`: \n"
-                              "The version string of '" + key + "': '" + value + "'"
-                              + " does not match with the last version string; "
-                              + "we suggest using the same version string across all foldernames.")
-            value_temp = value
-
-            cmd += "7z a ../${subid}" + str_sesid + "_" + \
-                key + "-" + value + ".zip" + " " + key + "\n"
-            # e.g., 7z a ../${subid}_${sesid}_fmriprep-0-0-0.zip fmriprep  # this is multi-ses
-
-    else:    # the yaml file does not have the section `zip_foldernames`:
-        raise Exception("The `container_config_yaml_file` does not contain"
-                        + " the section `zip_foldernames`. Please add this section!")
+    # start to generate 7z commands:
+    value_temp = ""
+    temp = 0
+    for key, value in dict_zip_foldernames.items():
+        # each key is a foldername to be zipped;
+        # each value is the version string;
+        temp = temp + 1
+        if (temp != 1) & (value_temp != value):    # not matching last value
+            warnings.warn("In section `zip_foldernames` in `container_config_yaml_file`: \n"
+                            "The version string of '" + key + "': '" + value + "'"
+                            + " does not match with the last version string; "
+                            + "we suggest using the same version string across all foldernames.")
+        value_temp = value
+
+        cmd += "7z a ../${subid}" + str_sesid + "_" + \
+            key + "-" + value + ".zip" + " " + key + "\n"
+        # e.g., 7z a ../${subid}_${sesid}_fmriprep-0-0-0.zip fmriprep  # this is multi-ses
 
     # return to original dir:
     cmd += "cd ..\n"
diff --git a/docs/source/preparation_config_yaml_file.rst b/docs/source/preparation_config_yaml_file.rst
index 3f0f811c..49edaf18 100644
--- a/docs/source/preparation_config_yaml_file.rst
+++ b/docs/source/preparation_config_yaml_file.rst
@@ -77,7 +77,9 @@ Instead, users are expected to define these in this section, **singularity_run**
 Example **singularity_run**
 -----------------------------------
 
-Below is example section **singularity_run** for ``fMRIPrep``::
+Below is example section **singularity_run** for ``fMRIPrep``:
+
+..  code-block:: yaml
 
     singularity_run:
         -w: "$BABS_TMPDIR"   # this is a placeholder for temporary workspace
@@ -368,15 +370,50 @@ Section ``zip_foldernames``
 This section defines the name(s) of the expected output folder(s).
 BABS will zip those folder(s) into separate zip file(s).
 
-Example section **zip_foldernames** for ``fMRIPrep``::
+Here we provide two examples. :ref:`Example #1 <example_zip_foldernames_for_fmriprep_legacy_output_layout>`
+is for regular use cases,
+where the BIDS App will generate one or several folders that wrap all derivative files.
+Example use cases are ``fMRIPrep`` with legacy output layout, as well as ``QSIPrep`` and ``XCP-D``.
+
+If the BIDS App won't generate one or several folders that wrap all derivative files,
+users should ask BABS to create a folder as an extra layer by specifying ``$TO_CREATE_FOLDER: "true"``.
+We explain how to do so in :ref:`Exmample #2 <example_zip_foldernames_for_fmriprep_BIDS_output_layout>`.
+An example use case is ``fMRIPrep`` with BIDS output layout.
+
+
+.. _example_zip_foldernames_for_fmriprep_legacy_output_layout:
+
+Example #1: for ``fMRIPrep`` *legacy* output layout
+------------------------------------------------------
+
+Here we use ``fMRIPrep`` (*legacy* output layout) as an example to show you
+how to write this ``zip_foldernames`` section. For this case, all derivative files
+are wrapped in folders generated by fMRIPrep. Similar use cases are ``QSIPrep``
+(e.g., generating a folder called ``qsiprep``), and ``XCP-D`` (generating a folder called ``xcp_d``).
+
+Older versions of ``fMRIPrep`` (version < 21.0) generate
+`legacy output layout <https://fmriprep.org/en/stable/outputs.html#legacy-layout>`_
+which looks like below::
+
+    <output_dir>/
+        fmriprep/
+        freesurfer/
+
+In this case, ``fMRIPrep`` generates two folders, ``fmriprep`` and ``freesurfer``,
+which include all derivatives. Therefore, we can directly tell BABS the expected foldernames,
+without asking BABS to create them.
+
+Example section **zip_foldernames** for ``fMRIPrep`` *legacy* output layout:
+
+..  code-block:: yaml
+    :linenos:
 
     zip_foldernames:
         fmriprep: "20-2-3"
         freesurfer: "20-2-3"
 
-As you can see in this example, we expect that fMRIPrep will generate two folders,
-one is called ``fmriprep``, the other is called ``freesurfer``.
-If there is only one expected output folder, simply provide only one.
+Here, we write the expected folders in line #2 and #3.
+For other BIDS Apps, if there is only one expected output folder, simply provide only one.
 
 In addition to the folder name(s), please also add the version of the BIDS App as the value.
 
@@ -389,16 +426,75 @@ Here, ``${sub-id}`` is the subject ID (e.g., ``sub-01``),
 and ``${ses-id}`` is the session ID (e.g., ``ses-A``).
 In other words, each subject (or session) will have their specific zip file(s).
 
-Other detailed instructions:
+
+.. _example_zip_foldernames_for_fmriprep_BIDS_output_layout:
+
+Example #2: for ``fMRIPrep`` *BIDS* output layout: asking BABS to create additional output folder
+---------------------------------------------------------------------------------------------------
+
+Recent ``fMRIPrep`` (version >= 21.0) uses
+`BIDS output layout <https://fmriprep.org/en/stable/outputs.html#layout>`_
+which looks like below::
+
+    <output_dir>/
+        logs/
+        sub-<label>/
+        sub-<label>.html
+        dataset_description.json
+        .bidsignore
+
+As you can see, there are files like ``sub-<label>.html`` and ``dataset_description.json``
+which do not belong to any folders (except ``<output_dir>``,
+which is a standard BIDS output directory).
+However, BABS expects there are
+one or more folders in ``<output_dir>`` that are generated by the BIDS App,
+and wrap all derivative files,
+so that BABS can directly zip these "wrapper" folders.
+Therefore, users need to ask BABS to create an additional folder to wrap all the derivatives.
+
+Example section **zip_foldernames** for ``fMRIPrep`` *BIDS* output layout:
+
+..  code-block:: yaml
+    :linenos:
+
+    zip_foldernames:
+        $TO_CREATE_FOLDER: "true"
+        fmriprep: "23-1-3"    
+
+Line #2 ``$TO_CREATE_FOLDER: "true"`` asks BABS to create an additional folder,
+i.e., ``fmriprep`` specified in line #3, to wrap all derivatives.
+In this way, the output will look like below::
+
+    <output_dir>/fmriprep/
+        logs/
+        sub-<label>/
+        sub-<label>.html
+        dataset_description.json
+        .bidsignore
+
+Note that all derivatives will locate in the "wrapper" folder called ``fmriprep``.
+BABS will zip this folder into zip file ``${sub-id}_${ses-id}_fmriprep-23-1-3.zip``.
+
+In addition, when using ``$TO_CREATE_FOLDER: "true"``,
+please only provide one foldername for BABS to create.
+
+Other detailed instructions
+---------------------------------
 
 * The version number should be consistent as that in *image NAME* when :ref:`create-a-container-datalad-dataset`.
-  For this example, you probably use ``fmriprep-20-2-3`` for *image NAME*.
-* When calling ``babs-init``, argument ``--container-name`` should use the same version too,
-  i.e., ``--container-name fmriprep-20-2-3`` for current example.
+  
+    * In example #1, you probably use ``fmriprep-20-2-3`` for *image NAME*;
+    * In example #2, you probably use ``fmriprep-23-1-3`` for *image NAME*.
+
+* When calling ``babs-init``, argument ``--container-name`` should use the same version too, i.e.,
+  
+    * ``--container-name fmriprep-20-2-3`` in example #1;
+    * ``--container-name fmriprep-23-1-3`` in example #2;
+
 * Please use dashes ``-`` instead of dots ``.`` when indicating the version number,
   e.g., ``20-2-3`` instead of ``20.2.3``.
 * If there are multiple folders to zip, we recommend using the consistent version string across these folders.
-  In this example case, the ``fMRIPrep`` BIDS App's version is ``20.2.3``, so we specify ``20-2-3`` for
+  In example #1, the ``fMRIPrep`` BIDS App's version is ``20.2.3``, so we specify ``20-2-3`` for
   both folders ``fmriprep`` and ``freesurfer``,
   although the version of ``FreeSurfer`` included in this ``fMRIPrep`` may not be ``20.2.3``.
 
@@ -413,7 +509,9 @@ and the interpreting shell for executing the job script.
 Example section **cluster_resources**
 ----------------------------------------
 
-Example section **cluster_resources** for ``QSIPrep``::
+Example section **cluster_resources** for ``QSIPrep``:
+
+..  code-block:: yaml
 
     cluster_resources:
         interpreting_shell: /bin/bash
@@ -553,7 +651,9 @@ bash commands that are required by job running. An example would be to activate
 however, different clusters may require different commands to do so. Therefore, BABS asks the user to
 provide it.
 
-Example section **script_preamble** for a specific cluster::
+Example section **script_preamble** for a specific cluster:
+
+..  code-block:: yaml
 
     script_preamble: |
         source ${CONDA_PREFIX}/bin/activate babs    # Penn Med CUBIC cluster; replace 'babs' with your conda env name
@@ -598,7 +698,9 @@ to (saved in) the output RIA (i.e., a permanent storage) where your BABS project
     We recommend using space that automatically cleans after the job finishes especially for large-scale dataset
     which has a large amount of jobs to do.
 
-Example section **job_compute_space**::
+Example section **job_compute_space**:
+
+..  code-block:: yaml
 
     job_compute_space: "${CBICA_TMPDIR}"   # Penn Med CUBIC cluster tmp space
 
@@ -639,7 +741,9 @@ You may have a dataset where not all the subjects (and sessions) have the requir
 running the BIDS App. You can simply provide this list of required files, and BABS will exclude those
 subjects and sessions who don't have any of listed required files.
 
-Example section **required_files** for ``fMRIPrep``::
+Example section **required_files** for ``fMRIPrep``:
+
+..  code-block:: yaml
 
     required_files:
         $INPUT_DATASET_#1:
@@ -683,7 +787,9 @@ This section is optional.
 This section is to define a list of alert messages to be searched in log files,
 and these messages may indicates failure of a job.
 
-Example section **alert_log_messages** for fMRIPrep::
+Example section **alert_log_messages** for fMRIPrep:
+
+..  code-block:: yaml
 
     alert_log_messages:
         stdout:
diff --git a/notebooks/README.md b/notebooks/README.md
index 8357b6b0..4e4cbc2c 100644
--- a/notebooks/README.md
+++ b/notebooks/README.md
@@ -16,13 +16,27 @@
 | [link](eg_toybidsapp-0-0-7_rawBIDS_sge_cubic.yaml) | toy BIDS App | 0.0.7 |for processing raw BIDS dataset | one raw BIDS dataset | SGE | |
 | [link](eg_toybidsapp-0-0-7_rawBIDS_slurm_msi.yaml) | toy BIDS App | 0.0.7 |for processing raw BIDS dataset | one raw BIDS dataset | Slurm | |
 | [link](eg_toybidsapp-0-0-7_zipped_sge_cubic.yaml) | toy BIDS App | 0.0.7 |for processing zipped BIDS derivatives dataset | one zipped BIDS derivatives dataset | SGE | |
+| [link](eg_toybidsapp-0-0-7_zipped_slurm_msi.yaml) | toy BIDS App | 0.0.7 |for processing zipped BIDS derivatives dataset | one zipped BIDS derivatives dataset | Slurm | |
 | [link](eg_fmriprep-20-2-3_full_sge_cubic.yaml) | fMRIPrep | 20.2.3 | Full run of fMRIPrep | one raw BIDS dataset | SGE | |
 | [link](eg_fmriprep-20-2-3_anatonly_sge_cubic.yaml) | fMRIPrep | 20.2.3 | fMRIPrep `--anat-only` mode | one raw BIDS dataset | SGE | |
 | [link](eg_fmriprep-20-2-3_ingressed-fs_sge_cubic.yaml) | fMRIPrep | 20.2.3 | fMRIPrep with FreeSurfer results ingressed | one raw BIDS dataset + one zipped BIDS derivatives dataset (of FreeSurfer results) | SGE | |
 | [link](eg_fmriprep-20-2-3_sloppy_sge_cubic.yaml) | fMRIPrep | 20.2.3 | fMRIPrep `--sloppy` mode | one raw BIDS dataset | SGE | ⚠️ WARNING: only for testing! ⚠️ |
 | [link](eg_fmriprep-20-2-3_sloppy_slurm_msi.yaml) | fMRIPrep | 20.2.3 | fMRIPrep `--sloppy` mode | one raw BIDS dataset | Slurm | ⚠️ WARNING: only for testing! ⚠️ |
-| [link](eg_fmriprepfake-0-1-1_full_sge_cubic.yaml) | fmriprep-fake | 0.1.1 | fmriprep-fake, mimicking legend output layout of fMRIPrep | one raw BIDS dataset | SGE | |
-| [link](eg_qsiprep-0-16-0RC3_sloppy_sge_cubic.yaml) | QSIPrep | 0.16.0RC3 | QSIPrep `--sloppy` mode | one raw BIDS dataset | SGE | ⚠️ WARNING: only for testing! ⚠️ |
-| [link](eg_qsiprep-0-16-0RC3_sloppy_slurm_msi.yaml) | QSIPrep | 0.16.0RC3 | QSIPrep `--sloppy` mode | one raw BIDS dataset | Slurm | ⚠️ WARNING: only for testing! ⚠️ |
+| [link](eg_fmriprepfake-0-1-2_full_slurm_msi.yaml) | fmriprep-fake | 0.1.2 | fmriprep-fake, mimicking current *BIDS output layout* of fMRIPrep (v21.0+) | one raw BIDS dataset | Slurm | |
+| [link](eg_fmriprepfake-0-1-2_legacy-layout_slurm_msi.yaml) | fmriprep-fake | 0.1.2 | fmriprep-fake, mimicking *legacy output layout* of fMRIPrep (< v21.0) | one raw BIDS dataset | Slurm | |
+| [link](eg_fmriprepfake-0-1-2_anatonly_slurm_msi.yaml) | fmriprep-fake | 0.1.2 | fmriprep-fake, using `--anat-only` | one raw BIDS dataset | Slurm | ⚠️ WARNING: For version `0.1.2`, although `--anat-only` is on, the generated files won't be different and will still include fMRI derivatives. |
+| [link](eg_qsiprep-0-16-0RC3_sloppy_sge_cubic.yaml) | QSIPrep | 0.16.0RC3 | QSIPrep `--sloppy` mode | one raw BIDS dataset | SGE | ⚠️ WARNING: only for testing! |
+| [link](eg_qsiprep-0-16-0RC3_sloppy_slurm_msi.yaml) | QSIPrep | 0.16.0RC3 | QSIPrep `--sloppy` mode | one raw BIDS dataset | Slurm | ⚠️ WARNING: only for testing! |
 | [link](eg_xcpd-0-3-0_full_sge_cubic.yaml ) | XCP-D | 0.3.0 | XCP full run | one zipped BIDS derivatives dataset (of fMRIPrep results) | SGE | |
 
+### BIDS App links
+| BIDS App | Function | Docker Hub | Docs | Notes | 
+| :-- | :--|:-- | :-- |:-- |
+| fMRIPrep | Preprocessing fMRI data | ___ | ___ | The default output layout changed in `21.0.0`. BABS YAML files for new BIDS layout and legacy layout are different. |
+| QSIPrep | Preprocessing dMRI data | [Docker Hub](https://hub.docker.com/r/pennbbl/qsiprep) | ____ | |
+| XCP-D | Post-processing fMRI data | ____ | _____ | The 0.4.0 version is labeled as `04.0` on Docker Hub. |
+| toy BIDS App | Quick test of BABS | ____ | _____ | |
+| fmriprep-fake | Mimics fMRIPrep output layout and generates fake derivatives, for quick test | [Docker Hub](https://hub.docker.com/r/djarecka/fmriprep_fake); Version 0.1.2 is available [here](https://hub.docker.com/r/chenyingzhao/fmriprep_fake) | see its [GitHub repo](https://github.com/djarecka/fmriprep-fake) |  |
+
+* fMRI = functional MRI
+* dMRI = diffusion MRI
diff --git a/notebooks/eg_fmriprep-20-2-3_anatonly_sge_cubic.yaml b/notebooks/eg_fmriprep-20-2-3_anatonly_sge_cubic.yaml
index 9942ce12..9a7d6b3a 100644
--- a/notebooks/eg_fmriprep-20-2-3_anatonly_sge_cubic.yaml
+++ b/notebooks/eg_fmriprep-20-2-3_anatonly_sge_cubic.yaml
@@ -45,6 +45,7 @@ singularity_run:
 
 # Output foldername(s) to be zipped, and the BIDS App version to be included in the zip filename(s):
 #   We use fMRIPrep's version string when zipping 'freesurfer' folder.
+#   WARNING: we will only save `freesurfer` folder, and won't save `fmriprep` folder (though it will be generated)
 zip_foldernames:
     freesurfer: "20-2-3"   # folder 'freesurfer' will be zipped into 'sub-xx_ses-yy_freesurfer-20-2-3.zip'
 
diff --git a/notebooks/eg_fmriprep-20-2-3_ingressed-fs-sloppy_sge_cubic.yaml b/notebooks/eg_fmriprep-20-2-3_ingressed-fs-sloppy_sge_cubic.yaml
new file mode 100644
index 00000000..5f031d82
--- /dev/null
+++ b/notebooks/eg_fmriprep-20-2-3_ingressed-fs-sloppy_sge_cubic.yaml
@@ -0,0 +1,66 @@
+# This is an example config yaml file for:
+#   BIDS App:         fMRIPrep ("fmriprep")
+#   BIDS App version: 20.2.3
+#   Task:             Preprocessing fMRI data with FreeSurfer results ingressed, however in a sloppy mode!
+#   Which system:     SGE
+#   Tested on which cluster:  PennMed CUBIC cluster
+
+# WARNING!!!
+#   This is in `--sloppy` mode, which is for testing ONLY, NOT for generating productions used for research!
+
+# WARNING!!!
+#   This is only an example, which may not necessarily fit your purpose,
+#   or be an optimized solution for your case,
+#   or be compatible to the BIDS App version you're using.
+#   Therefore, please change and tailor it for your case before use it!!!
+
+# Arguments in `singularity run`:
+#   In this example, we assume:
+#   1. You used BABS to run `fMRIPrep --anat-only` w/ fMRIPrep version 20.2.3, which used legacy output layout
+#   2. From 1, you have got output folder called `freesurfer` (i.e., `zip_foldernames`: `freesurfer`)
+#   3. When running `babs-init` for current use case, argument `--input` for `babs-init` is as below:
+#     --input BIDS <path/to/raw_BIDS_dataset>    # 1st input dataset \
+#     --input freesurfer <path/to/cloned_freesurfer_output_ria>    # 2nd input dataset \
+singularity_run:
+    $INPUT_PATH: inputs/data/BIDS   # the key `$INPUT_PATH` is a placeholder, which must be included first as there are two input datasets
+    -w: "$BABS_TMPDIR"   # this is a placeholder. To be changed to `${PWD}/.git/tmp/wkdir`
+    --n_cpus: '1'
+    --stop-on-first-crash: ""
+    --fs-license-file: "/cbica/projects/BABS/software/FreeSurfer/license.txt"  # [FIX ME] path to FS license file
+    --skip-bids-validation: ""
+    --output-spaces: MNI152NLin6Asym:res-2
+    --force-bbr: ""
+    --cifti-output: 91k
+    -v: "-v"
+    --fs-subjects-dir: inputs/data/freesurfer/freesurfer
+    --sloppy: ''      # ADD THIS WHEN TEST RUN!
+
+# Output foldername(s) to be zipped, and the BIDS App version to be included in the zip filename(s):
+zip_foldernames:
+    fmriprep: "20-2-3"     # folder 'fmriprep' will be zipped into 'sub-xx_(ses-yy_)fmriprep-20-2-3.zip'
+
+cluster_resources:
+    interpreting_shell: /bin/bash
+    hard_memory_limit: 24G
+    number_of_cpus: '2'
+    temporary_disk_space: 200G
+    customized_text: |
+        #$ -R y
+        #$ -l hostname=!compute-fed*
+# Notes: Above `customized_text` is Penn Med CUBIC cluster specific.
+#   So it's probably not relevant for other clusters
+
+# Necessary commands to be run first:
+script_preamble: |
+    source ${CONDA_PREFIX}/bin/activate mydatalad    # [FIX ME] Penn Med CUBIC cluster; replace 'mydatalad' with your conda env name
+
+# Where to run the jobs:
+job_compute_space: "${CBICA_TMPDIR}"   # Penn Med CUBIC cluster tmp space
+
+# Below is to filter out subjects (or sessions). Only those with required files will be kept.
+required_files:
+    $INPUT_DATASET_#1:
+        - "func/*_bold.nii*"
+        - "anat/*_T1w.nii*"
+
+# `alert_log_messages`: Here we did not provide examples for section `alert_log_messages`. However feel free to add it!
diff --git a/notebooks/eg_fmriprep-20-2-3_ingressed-fs_sge_cubic.yaml b/notebooks/eg_fmriprep-20-2-3_ingressed-fs_sge_cubic.yaml
index 8ce8491f..869e7225 100644
--- a/notebooks/eg_fmriprep-20-2-3_ingressed-fs_sge_cubic.yaml
+++ b/notebooks/eg_fmriprep-20-2-3_ingressed-fs_sge_cubic.yaml
@@ -1,46 +1,62 @@
-# Below is example config yaml file for fMRIPrep ingressed freesurfer:
+# This is an example config yaml file for:
+#   BIDS App:         fMRIPrep ("fmriprep")
+#   BIDS App version: 20.2.3
+#   Task:             Preprocessing fMRI data with FreeSurfer results ingressed
+#   Which system:     SGE
+#   Tested on which cluster:  PennMed CUBIC cluster
 
+# WARNING!!!
+#   This is only an example, which may not necessarily fit your purpose,
+#   or be an optimized solution for your case,
+#   or be compatible to the BIDS App version you're using.
+#   Therefore, please change and tailor it for your case before use it!!!
 
+# Arguments in `singularity run`:
+#   In this example, we assume:
+#   1. You used BABS to run `fMRIPrep --anat-only` w/ fMRIPrep version 20.2.3, which used legacy output layout
+#   2. From 1, you have got output folder called `freesurfer` (i.e., `zip_foldernames`: `freesurfer`)
+#   3. When running `babs-init` for current use case, argument `--input` for `babs-init` is as below:
+#     --input BIDS <path/to/raw_BIDS_dataset>    # 1st input dataset \
+#     --input freesurfer <path/to/cloned_freesurfer_output_ria>    # 2nd input dataset \
 singularity_run:
     $INPUT_PATH: inputs/data/BIDS   # the key `$INPUT_PATH` is a placeholder, which must be included first as there are two input datasets
     -w: "$BABS_TMPDIR"   # this is a placeholder. To be changed to `${PWD}/.git/tmp/wkdir`
     --n_cpus: '1'
     --stop-on-first-crash: ""
-    --fs-license-file: "/cbica/projects/BABS/software/FreeSurfer/license.txt"  # path to FS license file
+    --fs-license-file: "/cbica/projects/BABS/software/FreeSurfer/license.txt"  # [FIX ME] path to FS license file
     --skip-bids-validation: ""
     --output-spaces: MNI152NLin6Asym:res-2
     --force-bbr: ""
     --cifti-output: 91k
     -v: "-v"
     --fs-subjects-dir: inputs/data/freesurfer/freesurfer
-    --sloppy: ''      # ADD THIS WHEN TEST RUN!
 
 # Output foldername(s) to be zipped, and the BIDS App version to be included in the zip filename(s):
 zip_foldernames:
-    fmriprep: "20-2-3"     # folder 'fmriprep' will be zipped into 'sub-xx_ses-yy_fmriprep-20-2-3.zip'
+    fmriprep: "20-2-3"     # folder 'fmriprep' will be zipped into 'sub-xx_(ses-yy_)fmriprep-20-2-3.zip'
 
 cluster_resources:
-    interpreting_shell: /bin/bash   # "-S /bin/bash" on cubic
-    hard_memory_limit: 24G   # "-l h_vmem=24G" on cubic
-    number_of_cpus: '2'  # "-pe threaded 2" on cubic
-    temporary_disk_space: 200G   # "-l tmpfree=200G" on cubic
+    interpreting_shell: /bin/bash
+    hard_memory_limit: 24G
+    number_of_cpus: '2'
+    temporary_disk_space: 200G
     customized_text: |
         #$ -R y
         #$ -l hostname=!compute-fed*
 # Notes: Above `customized_text` is Penn Med CUBIC cluster specific.
 #   So it's probably not relevant for other clusters
 
-# Users need to add their customized bash command below,
-#   they will be used as preambles in `participant_job.sh`
-#   the commands should not be quoted!
+# Necessary commands to be run first:
 script_preamble: |
-    source ${CONDA_PREFIX}/bin/activate mydatalad    # Penn Med CUBIC cluster; replace 'mydatalad' with your conda env name
-    echo "I am running BABS."   # this is an example command to show how to add another line; not necessary to include.
+    source ${CONDA_PREFIX}/bin/activate mydatalad    # [FIX ME] Penn Med CUBIC cluster; replace 'mydatalad' with your conda env name
 
 # Where to run the jobs:
 job_compute_space: "${CBICA_TMPDIR}"   # Penn Med CUBIC cluster tmp space
 
+# Below is to filter out subjects (or sessions). Only those with required files will be kept.
 required_files:
     $INPUT_DATASET_#1:
         - "func/*_bold.nii*"
-        - "anat/*_T1w.nii*"
\ No newline at end of file
+        - "anat/*_T1w.nii*"
+
+# `alert_log_messages`: Here we did not provide examples for section `alert_log_messages`. However feel free to add it!
diff --git a/notebooks/eg_fmriprep-20-2-3_sloppy-no-fs_sge_cubic.yaml b/notebooks/eg_fmriprep-20-2-3_sloppy-no-fs_sge_cubic.yaml
new file mode 100644
index 00000000..5b784e98
--- /dev/null
+++ b/notebooks/eg_fmriprep-20-2-3_sloppy-no-fs_sge_cubic.yaml
@@ -0,0 +1,80 @@
+# This is an example config yaml file for:
+#   BIDS App:         fMRIPrep ("fmriprep")
+#   BIDS App version: 20.2.3
+#   Task:             `--sloppy` mode + without FreeSurfer reconstruction
+#   Which system:     SGE
+#   Tested on which cluster:  Penn Med CUBIC cluster
+
+# WARNING!!!
+#   This is only an example, which may not necessarily fit your purpose,
+#   or be an optimized solution for your case,
+#   or be compatible to the BIDS App version you're using.
+#   Therefore, please change and tailor it for your case before use it!!!
+# WARNING!!!
+#   We'll use `--sloppy` testing mode of fMRIPrep.
+#   Therefore this YAML file should only be used for testing purpose.
+#   You should NOT use this YAML file to generate formal results!
+
+# Arguments when executing the BIDS App using `singularity run`:
+singularity_run:
+    -w: "$BABS_TMPDIR"   # this is a placeholder. To be changed to `${PWD}/.git/tmp/wkdir`
+    --n_cpus: '1'
+    --stop-on-first-crash: ""
+    --fs-license-file: "/cbica/projects/BABS/software/FreeSurfer/license.txt"  # [FIX ME] path to FS license file
+    --skip-bids-validation: ""
+    --output-spaces: "MNI152NLin6Asym:res-2"   # for two output spaces: e.g., "MNI152NLin6Asym:res-2 MNI152NLin2009cAsym"
+    --force-bbr: ""
+    # --cifti-output: 91k    # probably not needed, as there is no FS recon
+    -v: '-v'   # this is for double "-v"
+    --sloppy: ''      # WARNING: use this only when testing
+    --fs-no-reconall: ''   # WARNING: use this only when testing
+
+# Output foldername(s) to be zipped, and the BIDS App version to be included in the zip filename(s):
+#   per `--fs-no-reconall`, there won't be an output folder called `freesurfer`
+zip_foldernames:
+    fmriprep: "20-2-3"   # folder 'fmriprep' will be zipped into 'sub-xx_ses-yy_fmriprep-20-2-3.zip'
+
+cluster_resources:
+    interpreting_shell: /bin/bash   # --> "#!/bin/bash"
+    hard_memory_limit: 25G   # --> "#$ -l h_vmem=25G"
+    temporary_disk_space: 200G   # --> "#$ -l tmpfree=200G"  # this is highly-recommended on CUBIC cluster
+    customized_text: |
+        #$ -R y
+        #$ -l hostname=!compute-fed*
+# Notes: Above `customized_text` is Penn Med CUBIC cluster specific.
+#   So it's probably not relevant for other clusters
+
+# Users need to add their customized bash command below,
+#   they will be used as preambles in `participant_job.sh`
+#   the commands should not be quoted!
+script_preamble: |
+    source ${CONDA_PREFIX}/bin/activate mydatalad    # [FIX ME] Penn Med CUBIC cluster; replace 'mydatalad' with your conda env name
+    echo "I am running BABS."   # [FIX ME] this is an example command to show how to add another line; not necessary to include.
+
+# ^^ conda env above: where the scripts generated by BABS will run
+#   not necessary the same one for running `babs-init`
+# ^^ based on what you need on your cluster; some people even don't use `conda`...
+# for MSI, might need to add command e.g., "module_load"
+
+# Where to run the jobs:
+job_compute_space: "${CBICA_TMPDIR}"   # [FIX ME] Penn Med CUBIC cluster tmp space
+
+# Below is to filter out subjects (or sessions)
+#   right now we only filter based on unzipped dataset
+required_files:
+    $INPUT_DATASET_#1:
+        - "func/*_bold.nii*"
+        - "anat/*_T1w.nii*"
+
+# Alert messages that might be found in log files of failed jobs:
+#   These messages may be helpful for debugging errors in failed jobs.
+alert_log_messages:
+    stdout:
+        - "Exception: No T1w images found for"  # probably not needed, after setting `required_files`
+        - "Excessive topologic defect encountered"
+        - "Cannot allocate memory"
+        - "mris_curvature_stats: Could not open file"
+        - "Numerical result out of range"
+        - "fMRIPrep failed"
+    # stderr:
+    #     - "xxxxx"
diff --git a/notebooks/eg_fmriprep-20-2-3_sloppy_sge_cubic.yaml b/notebooks/eg_fmriprep-20-2-3_sloppy_sge_cubic.yaml
index 81c5919f..b105efb9 100644
--- a/notebooks/eg_fmriprep-20-2-3_sloppy_sge_cubic.yaml
+++ b/notebooks/eg_fmriprep-20-2-3_sloppy_sge_cubic.yaml
@@ -1,10 +1,9 @@
 # This is an example config yaml file for:
 #   BIDS App:         fMRIPrep ("fmriprep")
 #   BIDS App version: 20.2.3
-#   Task:             `--sloppy` mode + without FreeSurfer reconstruction
+#   Task:             `--sloppy` mode
 #   Which system:     SGE
 #   Tested on which cluster:  Penn Med CUBIC cluster
-# fMRIPrep's Docker image is publicly available at: https://hub.docker.com/r/nipreps/fmriprep/
 
 # WARNING!!!
 #   This is only an example, which may not necessarily fit your purpose,
@@ -19,25 +18,26 @@
 # Arguments when executing the BIDS App using `singularity run`:
 singularity_run:
     -w: "$BABS_TMPDIR"   # this is a placeholder. To be changed to `${PWD}/.git/tmp/wkdir`
-    --n_cpus: '1'
+    --n_cpus: '1'    # seems like fMRIPrep 20.2.X that includes freesurfer recon, cannot go more than 1 cpus...
     --stop-on-first-crash: ""
     --fs-license-file: "/cbica/projects/BABS/software/FreeSurfer/license.txt"  # [FIX ME] path to FS license file
-    --skip-bids-validation: Null  # Null or NULL is also a placeholder
+    --skip-bids-validation: ""
     --output-spaces: "MNI152NLin6Asym:res-2"   # for two output spaces: e.g., "MNI152NLin6Asym:res-2 MNI152NLin2009cAsym"
     --force-bbr: ""
+    --cifti-output: 91k
     -v: '-v'   # this is for double "-v"
     --sloppy: ''      # WARNING: use this only when testing
-    --fs-no-reconall: ''   # WARNING: use this only when testing
 
 # Output foldername(s) to be zipped, and the BIDS App version to be included in the zip filename(s):
-#   per `--fs-no-reconall`, there won't be an output folder called `freesurfer`
 zip_foldernames:
-    fmriprep: "20-2-3"   # folder 'fmriprep' will be zipped into 'sub-xx_ses-yy_fmriprep-20-2-3.zip'
+    fmriprep: "20-2-3"   # folder 'fmriprep' will be zipped into 'sub-xx_(ses-yy_)fmriprep-20-2-3.zip'
+    freesurfer: "20-2-3"   # folder 'freesurfer' will be zipped into 'sub-xx_(ses-yy_)freesurfer-20-2-3.zip'
 
 cluster_resources:
-    interpreting_shell: /bin/bash   # --> "#!/bin/bash"
-    hard_memory_limit: 25G   # --> "#$ -l h_vmem=25G"
-    temporary_disk_space: 200G   # --> "#$ -l tmpfree=200G"  # this is highly-recommended on CUBIC cluster
+    interpreting_shell: /bin/bash
+    hard_memory_limit: 25G
+    temporary_disk_space: 200G
+    hard_runtime_limit: "96:00:00"
     customized_text: |
         #$ -R y
         #$ -l hostname=!compute-fed*
@@ -49,12 +49,6 @@ cluster_resources:
 #   the commands should not be quoted!
 script_preamble: |
     source ${CONDA_PREFIX}/bin/activate mydatalad    # [FIX ME] Penn Med CUBIC cluster; replace 'mydatalad' with your conda env name
-    echo "I am running BABS."   # [FIX ME] this is an example command to show how to add another line; not necessary to include.
-
-# ^^ conda env above: where the scripts generated by BABS will run
-#   not necessary the same one for running `babs-init`
-# ^^ based on what you need on your cluster; some people even don't use `conda`...
-# for MSI, might need to add command e.g., "module_load"
 
 # Where to run the jobs:
 job_compute_space: "${CBICA_TMPDIR}"   # [FIX ME] Penn Med CUBIC cluster tmp space
@@ -70,11 +64,8 @@ required_files:
 #   These messages may be helpful for debugging errors in failed jobs.
 alert_log_messages:
     stdout:
-        - "Exception: No T1w images found for"  # probably not needed, after setting `required_files`
         - "Excessive topologic defect encountered"
         - "Cannot allocate memory"
         - "mris_curvature_stats: Could not open file"
         - "Numerical result out of range"
         - "fMRIPrep failed"
-    # stderr:
-    #     - "xxxxx"
diff --git a/notebooks/eg_fmriprep-20-2-3_sloppy_slurm_msi.yaml b/notebooks/eg_fmriprep-20-2-3_sloppy_slurm_msi.yaml
index 0d877816..c40a98dc 100644
--- a/notebooks/eg_fmriprep-20-2-3_sloppy_slurm_msi.yaml
+++ b/notebooks/eg_fmriprep-20-2-3_sloppy_slurm_msi.yaml
@@ -41,8 +41,7 @@ cluster_resources:
     temporary_disk_space: 200G    # --> "#SBATCH --tmp=200G"
     hard_runtime_limit: "72:00:00"    # --> "--time=72:00:00", i.e., 3 days.  Should NOT large than partition's time limit!
     customized_text: |
-        #SBATCH -p k40
-# Other choices of job partitions on MSI: amd2tb,ram256g,v100,k40
+        #SBATCH -p amd2tb,ram256g
 # Notes: Above `customized_text` is MSI Slurm cluster specific.
 #   So it may not be relevant for other clusters
 
@@ -53,11 +52,6 @@ script_preamble: |
     source /home/faird/shared/code/external/envs/miniconda3/load_miniconda3.sh   # [FIX ME] MSI cluster faird group. Replace filepath with yours.
     conda activate babs   # [FIX ME] replace 'babs' with your env variable name
 
-# ^^ conda env above: where the scripts generated by BABS will run
-#   not necessary the same one for running `babs-init`
-# ^^ based on what you need on your cluster; some people even don't use `conda`...
-# for MSI, might need to add command e.g., "module_load"
-
 # Where to run the jobs:
 job_compute_space: "/tmp"   # [FIX ME] MSI cluster
 
diff --git a/notebooks/eg_fmriprep-23-1-3_anatonly_sge_cubic.yaml b/notebooks/eg_fmriprep-23-1-3_anatonly_sge_cubic.yaml
new file mode 100644
index 00000000..50c029a4
--- /dev/null
+++ b/notebooks/eg_fmriprep-23-1-3_anatonly_sge_cubic.yaml
@@ -0,0 +1,67 @@
+# This is an example config yaml file for:
+#   BIDS App:         fMRIPrep ("fmriprep")
+#   BIDS App version: 23.1.3
+#   Task:             `--anat-only` mode
+#   Which system:     SGE
+#   Tested on which cluster:  PennMed CUBIC cluster
+
+# WARNING!!!
+#   This is only an example, which may not necessarily fit your purpose,
+#   or be an optimized solution for your case,
+#   or be compatible to the BIDS App version you're using.
+#   Therefore, please change and tailor it for your case before use it!!!
+
+# Arguments in `singularity run`:
+singularity_run:
+    -w: "$BABS_TMPDIR"   # this is a placeholder recognized by BABS.
+    --n_cpus: "1"
+    --stop-on-first-crash: ""
+    --fs-license-file: "/cbica/projects/BABS/software/FreeSurfer/license.txt"  # [FIX ME] path to FS license file
+    --skip-bids-validation: ""
+    --output-spaces: MNI152NLin6Asym:res-2   # TODO: needed? Only generated figures, not real images...
+    --force-bbr: ""   # TODO: needed?
+    -v: '-v'
+    --anat-only: ""   # only runs the anatomical workflows
+
+# Output foldername(s) to be zipped, and the BIDS App version to be included in the zip filename(s):
+#   As fMRIPrep will use BIDS output layout, we need to ask BABS to create a folder 'fmriprep_anat' to wrap all derivatives:
+zip_foldernames:
+    $TO_CREATE_FOLDER: "true"
+    fmriprep_anat: "23-1-3"   # folder 'fmriprep_anat' will be zipped into 'sub-xx_(ses-yy_)fmriprep_anat-23-1-3.zip'
+# Note: The generated data can also be used to provide FreeSurfer derivatives as input dataset when running fMRIPrep on fMRI data,
+#   i.e., for use case: fMRIPrep with FreeSurfer results ingressed.
+#   For that case, when using `babs-init`, for `--input`, please call this FreeSurfer derivatives dataset 'fmriprep_anat'.
+
+cluster_resources:
+    interpreting_shell: /bin/bash
+    hard_memory_limit: 25G
+    temporary_disk_space: 200G
+    hard_runtime_limit: "48:00:00"
+    customized_text: |
+        #$ -R y
+        #$ -l hostname=!compute-fed*
+# Notes: Above `customized_text` is Penn Med CUBIC cluster specific.
+#   So it's probably not relevant for other clusters
+
+# Necessary commands to be run first:
+script_preamble: |
+    source ${CONDA_PREFIX}/bin/activate mydatalad    # Penn Med CUBIC cluster; replace 'mydatalad' with your conda env name
+
+# Where to run the jobs:
+job_compute_space: "${CBICA_TMPDIR}"   # Penn Med CUBIC cluster tmp space
+
+# Below is to filter out subjects (or sessions). Only those with required files will be kept.
+#   Because of `--anat-only`, func bold data is not needed.
+required_files:
+    $INPUT_DATASET_#1:
+        - "anat/*_T1w.nii*"
+
+# Alert messages that might be found in log files of failed jobs:
+#   These messages may be helpful for debugging errors in failed jobs.
+alert_log_messages:
+    stdout:
+        - "Excessive topologic defect encountered"
+        - "Cannot allocate memory"
+        - "mris_curvature_stats: Could not open file"
+        - "Numerical result out of range"
+        - "fMRIPrep failed"
diff --git a/notebooks/eg_fmriprep-23-1-3_anatonly_slurm_msi.yaml b/notebooks/eg_fmriprep-23-1-3_anatonly_slurm_msi.yaml
new file mode 100644
index 00000000..2c897eee
--- /dev/null
+++ b/notebooks/eg_fmriprep-23-1-3_anatonly_slurm_msi.yaml
@@ -0,0 +1,67 @@
+# This is an example config yaml file for:
+#   BIDS App:         fMRIPrep ("fmriprep")
+#   BIDS App version: 23.1.3
+#   Task:             `--anat-only` mode
+#   Which system:     Slurm
+#   Tested on which cluster:  UMN MSI cluster
+
+# WARNING!!!
+#   This is only an example, which may not necessarily fit your purpose,
+#   or be an optimized solution for your case,
+#   or be compatible to the BIDS App version you're using.
+#   Therefore, please change and tailor it for your case before use it!!!
+
+# Arguments in `singularity run`:
+singularity_run:
+    -w: "$BABS_TMPDIR"   # this is a placeholder recognized by BABS.
+    --n_cpus: "1"
+    --stop-on-first-crash: ""
+    --fs-license-file: "/home/faird/zhaoc/software/FreeSurfer/license.txt"  # [FIX ME] path to FS license file
+    --skip-bids-validation: ""
+    --output-spaces: MNI152NLin6Asym:res-2   # TODO: needed? Only generated figures, not real images...
+    --force-bbr: ""   # TODO: needed?
+    -v: '-v'
+    --anat-only: ""   # only runs the anatomical workflows
+
+# Output foldername(s) to be zipped, and the BIDS App version to be included in the zip filename(s):
+#   As we are using BIDS output layout, we need to ask BABS to create a folder 'fmriprep_anat' to wrap all derivatives:
+zip_foldernames:
+    $TO_CREATE_FOLDER: "true"
+    fmriprep_anat: "23-1-3"   # folder 'fmriprep_anat' will be zipped into 'sub-xx_(ses-yy_)fmriprep_anat-23-1-3.zip'
+# Note: The generated data can also be used to provide FreeSurfer derivatives as input dataset when running fMRIPrep on fMRI data,
+#   i.e., for use case: fMRIPrep with FreeSurfer results ingressed.
+#   For that case, when using `babs-init`, for `--input`, please call this FreeSurfer derivatives dataset 'fmriprep_anat'.
+
+cluster_resources:
+    interpreting_shell: "/bin/bash -l"
+    hard_memory_limit: 25G
+    temporary_disk_space: 200G
+    hard_runtime_limit: "48:00:00"
+    customized_text: |
+        #SBATCH -p amd2tb,ram256g
+# Notes: Above `customized_text` is MSI Slurm cluster specific.
+#   So it may not be relevant for other clusters
+
+# Necessary commands to be run first:
+script_preamble: |
+    source /home/faird/shared/code/external/envs/miniconda3/load_miniconda3.sh   # [FIX ME] MSI cluster faird group. Replace filepath with yours.
+    conda activate babs   # [FIX ME] replace 'babs' with your env variable name
+
+# Where to run the jobs:
+job_compute_space: "/tmp"   # [FIX ME] MSI cluster
+
+# Below is to filter out subjects (or sessions). Only those with required files will be kept.
+#   Because of `--anat-only`, func bold data is not needed.
+required_files:
+    $INPUT_DATASET_#1:
+        - "anat/*_T1w.nii*"
+
+# Alert messages that might be found in log files of failed jobs:
+#   These messages may be helpful for debugging errors in failed jobs.
+alert_log_messages:
+    stdout:
+        - "Excessive topologic defect encountered"
+        - "Cannot allocate memory"
+        - "mris_curvature_stats: Could not open file"
+        - "Numerical result out of range"
+        - "fMRIPrep failed"
diff --git a/notebooks/eg_fmriprep-23-1-3_ingressed-fs-sloppy_sge_cubic.yaml b/notebooks/eg_fmriprep-23-1-3_ingressed-fs-sloppy_sge_cubic.yaml
new file mode 100644
index 00000000..7e43b82a
--- /dev/null
+++ b/notebooks/eg_fmriprep-23-1-3_ingressed-fs-sloppy_sge_cubic.yaml
@@ -0,0 +1,69 @@
+# This is an example config yaml file for:
+#   BIDS App:         fMRIPrep ("fmriprep")
+#   BIDS App version: 23.1.3
+#   Task:             Preprocessing fMRI data with FreeSurfer results ingressed, however in a sloppy mode!
+#   Which system:     SGE
+#   Tested on which cluster:  PennMed CUBIC cluster
+
+# WARNING!!!
+#   This is in `--sloppy` mode, which is for testing ONLY, NOT for generating productions used for research!
+
+# WARNING!!!
+#   This is only an example, which may not necessarily fit your purpose,
+#   or be an optimized solution for your case,
+#   or be compatible to the BIDS App version you're using.
+#   Therefore, please change and tailor it for your case before use it!!!
+
+# Arguments in `singularity run`:
+#   In this example, we assume:
+#   1. You used BABS to run `fMRIPrep --anat-only` w/ fMRIPrep version 23.1.3, and used current BIDS output layout (default);
+#   2. From 1, you have got output folder called `fmriprep_anat` (i.e., `zip_foldernames`: `fmriprep_anat`)
+#   3. When running `babs-init` for current use case, argument `--input` for `babs-init` is as below:
+#     --input BIDS <path/to/raw_BIDS_dataset>    # 1st input dataset \
+#     --input fmriprep_anat <path/to/cloned_fmriprep_anat_output_ria>    # 2nd input dataset \
+singularity_run:
+    $INPUT_PATH: inputs/data/BIDS   # the key `$INPUT_PATH` is a placeholder, which must be included first as there are two input datasets
+    -w: "$BABS_TMPDIR"   # this is a placeholder recognized by BABS.
+    --n_cpus: '1'
+    --stop-on-first-crash: ""
+    --fs-license-file: "/cbica/projects/BABS/software/FreeSurfer/license.txt"  # [FIX ME] path to FS license file
+    --skip-bids-validation: ""
+    --output-spaces: MNI152NLin6Asym:res-2
+    --force-bbr: ""
+    --cifti-output: 91k
+    -v: "-v"
+    --fs-subjects-dir: inputs/data/fmriprep_anat/fmriprep_anat/sourcedata/freesurfer
+    --sloppy: ''      # ADD THIS WHEN TEST RUN! TODO: remove this in a full run!
+
+# Output foldername(s) to be zipped, and the BIDS App version to be included in the zip filename(s):
+#   As we are using BIDS output layout, we need to ask BABS to create a folder 'fmriprep' to wrap all derivatives:
+zip_foldernames:
+    $TO_CREATE_FOLDER: "true"
+    fmriprep: "23-1-3"     # folder 'fmriprep' will be zipped into 'sub-xx_(ses-yy_)fmriprep-23-1-3.zip'
+
+cluster_resources:
+    interpreting_shell: /bin/bash
+    hard_memory_limit: 24G
+    number_of_cpus: '2'
+    temporary_disk_space: 200G
+    hard_runtime_limit: "96:00:00"   # note: max on MSI cluster  # TODO: what's preferred?
+    customized_text: |
+        #$ -R y
+        #$ -l hostname=!compute-fed*
+# Notes: Above `customized_text` is Penn Med CUBIC cluster specific.
+#   So it's probably not relevant for other clusters
+
+# Necessary commands to be run first:
+script_preamble: |
+    source ${CONDA_PREFIX}/bin/activate mydatalad    # Penn Med CUBIC cluster; replace 'mydatalad' with your conda env name
+
+# Where to run the jobs:
+job_compute_space: "${CBICA_TMPDIR}"   # Penn Med CUBIC cluster tmp space
+
+# Below is to filter out subjects (or sessions). Only those with required files will be kept.
+required_files:
+    $INPUT_DATASET_#1:
+        - "func/*_bold.nii*"
+        - "anat/*_T1w.nii*"
+
+# `alert_log_messages`: Here we did not provide examples for section `alert_log_messages`. However feel free to add it!
diff --git a/notebooks/eg_fmriprep-23-1-3_ingressed-fs-sloppy_slurm_msi.yaml b/notebooks/eg_fmriprep-23-1-3_ingressed-fs-sloppy_slurm_msi.yaml
new file mode 100644
index 00000000..441520cb
--- /dev/null
+++ b/notebooks/eg_fmriprep-23-1-3_ingressed-fs-sloppy_slurm_msi.yaml
@@ -0,0 +1,69 @@
+# This is an example config yaml file for:
+#   BIDS App:         fMRIPrep ("fmriprep")
+#   BIDS App version: 23.1.3
+#   Task:             Preprocessing fMRI data with FreeSurfer results ingressed, however in a sloppy mode!
+#   Which system:     Slurm
+#   Tested on which cluster:  UMN MSI cluster
+
+# WARNING!!!
+#   This is in `--sloppy` mode, which is for testing ONLY, NOT for generating productions used for research!
+
+# WARNING!!!
+#   This is only an example, which may not necessarily fit your purpose,
+#   or be an optimized solution for your case,
+#   or be compatible to the BIDS App version you're using.
+#   Therefore, please change and tailor it for your case before use it!!!
+
+# Arguments in `singularity run`:
+#   In this example, we assume:
+#   1. You used BABS to run `fMRIPrep --anat-only` w/ fMRIPrep version 23.1.3, and used current BIDS output layout (default);
+#   2. You have got output folder called `fmriprep_anat` (i.e., `zip_foldernames`: `fmriprep_anat`)
+#   3. When running `babs-init` for current use case, argument `--input` for `babs-init` is as below:
+#     --input BIDS <path/to/raw_BIDS_dataset>    # 1st input dataset \
+#     --input fmriprep_anat <path/to/cloned_fmriprep_anat_output_ria>    # 2nd input dataset \
+singularity_run:
+    $INPUT_PATH: inputs/data/BIDS   # the key `$INPUT_PATH` is a placeholder, which must be included first as there are two input datasets
+    -w: "$BABS_TMPDIR"   # this is a placeholder recognized by BABS.
+    --n_cpus: '1'
+    --stop-on-first-crash: ""
+    --fs-license-file: "/home/faird/zhaoc/software/FreeSurfer/license.txt"  # [FIX ME] path to FS license file
+    --skip-bids-validation: ""
+    --output-spaces: MNI152NLin6Asym:res-2
+    --force-bbr: ""
+    --cifti-output: 91k
+    -v: "-v"
+    --fs-subjects-dir: inputs/data/fmriprep_anat/fmriprep_anat/sourcedata/freesurfer
+    --sloppy: ''      # ADD THIS WHEN TEST RUN! TODO: remove this in a full run!
+
+# Output foldername(s) to be zipped, and the BIDS App version to be included in the zip filename(s):
+#   As we are using BIDS output layout, we need to ask BABS to create a folder 'fmriprep' to wrap all derivatives:
+zip_foldernames:
+    $TO_CREATE_FOLDER: "true"
+    fmriprep: "23-1-3"     # folder 'fmriprep' will be zipped into 'sub-xx_ses-yy_fmriprep-23-1-3.zip'
+
+cluster_resources:
+    interpreting_shell: "/bin/bash -l"
+    hard_memory_limit: 24G
+    number_of_cpus: '2'
+    temporary_disk_space: 200G
+    hard_runtime_limit: "96:00:00"   # note: max on MSI cluster  # TODO: what's preferred?
+    customized_text: |
+        #SBATCH -p amd2tb,ram256g
+# Notes: Above `customized_text` is MSI Slurm cluster specific.
+#   So it may not be relevant for other clusters
+
+# Necessary commands to be run first:
+script_preamble: |
+    source /home/faird/shared/code/external/envs/miniconda3/load_miniconda3.sh   # [FIX ME] MSI cluster faird group. Replace filepath with yours.
+    conda activate babs   # [FIX ME] replace 'babs' with your env variable name
+
+# Where to run the jobs:
+job_compute_space: "/tmp"   # [FIX ME] MSI cluster
+
+# Below is to filter out subjects (or sessions). Only those with required files will be kept.
+required_files:
+    $INPUT_DATASET_#1:
+        - "func/*_bold.nii*"
+        - "anat/*_T1w.nii*"
+
+# `alert_log_messages`: Here we did not provide examples for section `alert_log_messages`. However feel free to add it!
diff --git a/notebooks/eg_fmriprep-23-1-3_ingressed-fs_slurm_msi.yaml b/notebooks/eg_fmriprep-23-1-3_ingressed-fs_slurm_msi.yaml
new file mode 100644
index 00000000..d474651f
--- /dev/null
+++ b/notebooks/eg_fmriprep-23-1-3_ingressed-fs_slurm_msi.yaml
@@ -0,0 +1,65 @@
+# This is an example config yaml file for:
+#   BIDS App:         fMRIPrep ("fmriprep")
+#   BIDS App version: 23.1.3
+#   Task:             Preprocessing fMRI data with FreeSurfer results ingressed
+#   Which system:     Slurm
+#   Tested on which cluster:  UMN MSI cluster
+
+# WARNING!!!
+#   This is only an example, which may not necessarily fit your purpose,
+#   or be an optimized solution for your case,
+#   or be compatible to the BIDS App version you're using.
+#   Therefore, please change and tailor it for your case before use it!!!
+
+# Arguments in `singularity run`:
+#   In this example, we assume:
+#   1. You used BABS to run `fMRIPrep --anat-only` w/ fMRIPrep version 23.1.3, and used current BIDS output layout (default);
+#   2. You have got output folder called `fmriprep_anat` (i.e., `zip_foldernames`: `fmriprep_anat`)
+#   3. When running `babs-init` for current use case, argument `--input` for `babs-init` is as below:
+#     --input BIDS <path/to/raw_BIDS_dataset>    # 1st input dataset \
+#     --input fmriprep_anat <path/to/cloned_fmriprep_anat_output_ria>    # 2nd input dataset \
+singularity_run:
+    $INPUT_PATH: inputs/data/BIDS   # the key `$INPUT_PATH` is a placeholder, which must be included first as there are two input datasets
+    -w: "$BABS_TMPDIR"   # this is a placeholder recognized by BABS.
+    --n_cpus: '1'
+    --stop-on-first-crash: ""
+    --fs-license-file: "/home/faird/zhaoc/software/FreeSurfer/license.txt"  # [FIX ME] path to FS license file
+    --skip-bids-validation: ""
+    --output-spaces: MNI152NLin6Asym:res-2
+    --force-bbr: ""
+    --cifti-output: 91k
+    -v: "-v"
+    --fs-subjects-dir: inputs/data/fmriprep_anat/fmriprep_anat/sourcedata/freesurfer
+
+# Output foldername(s) to be zipped, and the BIDS App version to be included in the zip filename(s):
+#   As we are using BIDS output layout, we need to ask BABS to create a folder 'fmriprep' to wrap all derivatives:
+zip_foldernames:
+    $TO_CREATE_FOLDER: "true"
+    fmriprep: "23-1-3"     # folder 'fmriprep' will be zipped into 'sub-xx_ses-yy_fmriprep-23-1-3.zip'
+
+cluster_resources:
+    interpreting_shell: "/bin/bash -l"
+    hard_memory_limit: 24G
+    number_of_cpus: '2'
+    temporary_disk_space: 200G
+    hard_runtime_limit: "96:00:00"   # note: max on MSI cluster  # TODO: what's preferred?
+    customized_text: |
+        #SBATCH -p amd2tb,ram256g
+# Notes: Above `customized_text` is Penn Med CUBIC cluster specific.
+#   So it's probably not relevant for other clusters
+
+# Necessary commands to be run first:
+script_preamble: |
+    source /home/faird/shared/code/external/envs/miniconda3/load_miniconda3.sh   # [FIX ME] MSI cluster faird group. Replace filepath with yours.
+    conda activate babs   # [FIX ME] replace 'babs' with your env variable name
+
+# Where to run the jobs:
+job_compute_space: "/tmp"   # [FIX ME] MSI cluster
+
+# Below is to filter out subjects (or sessions). Only those with required files will be kept.
+required_files:
+    $INPUT_DATASET_#1:
+        - "func/*_bold.nii*"
+        - "anat/*_T1w.nii*"
+
+# `alert_log_messages`: Here we did not provide examples for section `alert_log_messages`. However feel free to add it!
diff --git a/notebooks/eg_fmriprep-23-1-3_sloppy_sge_cubic.yaml b/notebooks/eg_fmriprep-23-1-3_sloppy_sge_cubic.yaml
new file mode 100644
index 00000000..3f0099da
--- /dev/null
+++ b/notebooks/eg_fmriprep-23-1-3_sloppy_sge_cubic.yaml
@@ -0,0 +1,69 @@
+# This is an example config yaml file for:
+#   BIDS App:         fMRIPrep ("fmriprep")
+#   BIDS App version: 23.1.3
+#   Task:             `--sloppy` mode
+#   Which system:     SGE
+#   Tested on which cluster:  Penn Med CUBIC cluster
+
+# WARNING!!!
+#   This is only an example, which may not necessarily fit your purpose,
+#   or be an optimized solution for your case,
+#   or be compatible to the BIDS App version you're using.
+#   Therefore, please change and tailor it for your case before use it!!!
+# WARNING!!!
+#   We'll use `--sloppy` testing mode of fMRIPrep.
+#   Therefore this YAML file should only be used for testing purpose.
+#   You should NOT use this YAML file to generate formal results!
+
+# Arguments in `singularity run`:
+singularity_run:
+    -w: "$BABS_TMPDIR"   # this is a placeholder recognized by BABS.
+    --n_cpus: '1'
+    --stop-on-first-crash: ""
+    --fs-license-file: "/cbica/projects/BABS/software/FreeSurfer/license.txt"  # [FIX ME] path to FS license file
+    --skip-bids-validation: ""
+    --output-spaces: "MNI152NLin6Asym:res-2"
+    --force-bbr: ""
+    --cifti-output: 91k
+    -v: '-v'
+    --sloppy: ''      # WARNING: use this only when testing
+
+# Output foldername(s) to be zipped, and the BIDS App version to be included in the zip filename(s):
+#   As fMRIPrep will use BIDS output layout, we need to ask BABS to create a folder 'fmriprep' to wrap all derivatives:
+zip_foldernames:
+    $TO_CREATE_FOLDER: "true"
+    fmriprep: "23-1-3"   # folder 'fmriprep' will be zipped into 'sub-xx_(ses-yy_)fmriprep-23-1-3.zip'
+
+cluster_resources:
+    interpreting_shell: /bin/bash
+    hard_memory_limit: 25G
+    temporary_disk_space: 200G
+    hard_runtime_limit: "96:00:00"
+    customized_text: |
+        #$ -R y
+        #$ -l hostname=!compute-fed*
+# Notes: Above `customized_text` is Penn Med CUBIC cluster specific.
+#   So it's probably not relevant for other clusters
+
+# Necessary commands to be run first:
+script_preamble: |
+    source ${CONDA_PREFIX}/bin/activate mydatalad    # [FIX ME] Penn Med CUBIC cluster; replace 'mydatalad' with your conda env name
+
+# Where to run the jobs:
+job_compute_space: "${CBICA_TMPDIR}"   # [FIX ME] Penn Med CUBIC cluster tmp space
+
+# Below is to filter out subjects (or sessions). Only those with required files will be kept.
+required_files:
+    $INPUT_DATASET_#1:
+        - "func/*_bold.nii*"
+        - "anat/*_T1w.nii*"
+
+# Alert messages that might be found in log files of failed jobs:
+#   These messages may be helpful for debugging errors in failed jobs.
+alert_log_messages:
+    stdout:
+        - "Excessive topologic defect encountered"
+        - "Cannot allocate memory"
+        - "mris_curvature_stats: Could not open file"
+        - "Numerical result out of range"
+        - "fMRIPrep failed"
diff --git a/notebooks/eg_fmriprepfake-0-1-1_full_sge_cubic.yaml b/notebooks/eg_fmriprepfake-0-1-1_full_sge_cubic.yaml
deleted file mode 100644
index 46622b98..00000000
--- a/notebooks/eg_fmriprepfake-0-1-1_full_sge_cubic.yaml
+++ /dev/null
@@ -1,48 +0,0 @@
-# This is an example config yaml file for fmriprep-fake version 0.1.0.
-# fmriprep-fake's Docker image is publicly available at: https://hub.docker.com/r/djarecka/fmriprep_fake
-# fmriprep-fake generates fMRIPrep outputs without running fMRIPrep itself. You may use it to check fmriprep outputs.
-#     More details please see: https://github.com/djarecka/fmriprep-fake
-# Thanks to Dorota Jarecka for preparing and sharing this BIDS App!
-
-# Warning!!!
-#   This is only an example, which may not necessarily fit your purpose,
-#   or be an optimized solution for your case,
-#   or be compatible to the toy BIDS App version you're using.
-#   Therefore, please change and tailor it for your case before use it!!!
-
-# 'singularity_run': There is no such section for fmriprep-fake
-#   as all commands needed by fmriprep-fake have been handled by BABS.
-
-# Output foldername(s) to be zipped, and the BIDS App version to be included in the zip filename(s):
-zip_foldernames:
-    fmriprepfake: "0-1-1"   # folder 'fmriprepfake' will be zipped into 'sub-xx_ses-yy_fmriprepfake-0-1-1.zip'
-
-cluster_resources:
-    interpreting_shell: /bin/bash   # "-S /bin/bash" on cubic
-    hard_memory_limit: 2G   # "-l h_vmem=25G" on cubic
-    temporary_disk_space: 20G   # "-l tmpfree=50G" on cubic  # this is highly-recommended on cubic
-    hard_runtime_limit: "24:00:00"   # needed by cubic for PennLINC lab members; otherwise jobs will be sent to generic nodes 
-    customized_text: |
-        #$ -R y
-        #$ -l hostname=!compute-fed*
-# Notes: Above `customized_text` is Penn Med CUBIC cluster specific.
-#   So it's probably not relevant for other clusters
-
-# Users need to add their customized bash command below,
-#   they will be used as preambles in `participant_job.sh`
-#   the commands should not be quoted!
-script_preamble: |
-    source ${CONDA_PREFIX}/bin/activate mydatalad    # Penn Med CUBIC cluster; replace 'mydatalad' with your conda env name
-    echo "I am running BABS."   # this is an example command to show how to add another line; not necessary to include.
-
-# Where to run the jobs:
-job_compute_space: "${CBICA_TMPDIR}"   # Penn Med CUBIC cluster tmp space
-
-# Below is to filter out subjects (or sessions)
-#   right now we only filter based on unzipped dataset
-required_files:
-    $INPUT_DATASET_#1:
-        - "func/*_bold.nii*"
-        - "anat/*_T1w.nii*"
-
-# 'alert_log_messages': not to include this section for now.
diff --git a/notebooks/eg_fmriprepfake-0-1-2_anatonly_slurm_msi.yaml b/notebooks/eg_fmriprepfake-0-1-2_anatonly_slurm_msi.yaml
new file mode 100644
index 00000000..32a9c1ae
--- /dev/null
+++ b/notebooks/eg_fmriprepfake-0-1-2_anatonly_slurm_msi.yaml
@@ -0,0 +1,54 @@
+# This is an example config yaml file for:
+#   BIDS App:         fmriprep-fake
+#   BIDS App version: 0.1.2
+#   Task:             `--anat-only` mode
+#   Which system:     Slurm
+#   Tested on which cluster:  UMN MSI cluster
+
+# Warning!!!
+#   although `fmriprep-fake` version 0.1.2 takes argument `--anat-only`, it won't do anything different,
+#   and it will still generate all derivatives (including fMRI data derivatives)...
+#   Therefore, this is only for testing purpose!
+
+# Warning!!!
+#   This is only an example, which may not necessarily fit your purpose,
+#   or be an optimized solution for your case,
+#   or be compatible to the BIDS App version you're using.
+#   Therefore, please change and tailor it for your case before use it!!!
+
+# Arguments in `singularity run`:
+singularity_run:
+    --anat-only: ""
+
+# Output foldername(s) to be zipped, and the BIDS App version to be included in the zip filename(s):
+#   As we are using BIDS output layout, we need to ask BABS to create a folder 'fmriprep_anat' to wrap all derivatives:
+zip_foldernames:
+    $TO_CREATE_FOLDER: "true"
+    fmriprep_anat: "0-1-2"   # folder 'fmriprep_anat' will be zipped into 'sub-xx_(ses-yy_)fmriprep_anat-0-1-2.zip'
+
+# How much cluster resources it needs:
+cluster_resources:
+    interpreting_shell: "/bin/bash -l"
+    hard_memory_limit: 2G
+    temporary_disk_space: 20G
+    hard_runtime_limit: "20"   # 20min
+    customized_text: |
+        #SBATCH -p amd2tb,ram256g
+# Notes: Above `customized_text` is MSI Slurm cluster specific.
+#   So it may not be relevant for other clusters
+
+# Necessary commands to be run first:
+script_preamble: |
+    source /home/faird/shared/code/external/envs/miniconda3/load_miniconda3.sh   # [FIX ME] MSI cluster faird group. Replace filepath with yours.
+    conda activate babs   # [FIX ME] replace 'babs' with your env variable name
+
+# Where to run the jobs:
+job_compute_space: "/tmp"   # [FIX ME] MSI cluster
+
+# Below is to filter out subjects (or sessions). Only those with required files will be kept.
+#   Because of `--anat-only`, func bold data is not needed.
+required_files:
+    $INPUT_DATASET_#1:
+        - "anat/*_T1w.nii*"
+
+# 'alert_log_messages': not included in this example, but you may add it!
diff --git a/notebooks/eg_fmriprepfake-0-1-2_full_slurm_msi.yaml b/notebooks/eg_fmriprepfake-0-1-2_full_slurm_msi.yaml
new file mode 100644
index 00000000..5525dceb
--- /dev/null
+++ b/notebooks/eg_fmriprepfake-0-1-2_full_slurm_msi.yaml
@@ -0,0 +1,50 @@
+# This is an example config yaml file for:
+#   BIDS App:         fmriprep-fake
+#   BIDS App version: 0.1.2
+#   Task:             regular mode, generating BIDS output layout
+#   Which system:     Slurm
+#   Tested on which cluster:  UMN MSI cluster
+
+# Warning!!!
+#   This is only an example, which may not necessarily fit your purpose,
+#   or be an optimized solution for your case,
+#   or be compatible to the BIDS App version you're using.
+#   Therefore, please change and tailor it for your case before use it!!!
+
+# 'singularity_run': There is no such section for fmriprep-fake
+#   as all commands needed by fmriprep-fake have been handled by BABS.
+
+# Output foldername(s) to be zipped, and the BIDS App version to be included in the zip filename(s):
+#   As we are using BIDS output layout, we need to ask BABS to create a folder 'fmriprepfake' to wrap all derivatives:
+zip_foldernames:
+    $TO_CREATE_FOLDER: "true"
+    fmriprepfake: "0-1-2"   # folder 'fmriprepfake' will be zipped into 'sub-xx_ses-yy_fmriprepfake-0-1-2.zip'
+
+cluster_resources:
+    interpreting_shell: "/bin/bash -l"
+    hard_memory_limit: 2G
+    temporary_disk_space: 20G
+    hard_runtime_limit: "20"   # 20min
+    customized_text: |
+        #SBATCH -p amd2tb,ram256g
+# Notes: Above `customized_text` is MSI Slurm cluster specific.
+#   So it may not be relevant for other clusters
+
+# Users need to add their customized bash command below,
+#   they will be used as preambles in `participant_job.sh`
+#   the commands should not be quoted!
+script_preamble: |
+    source /home/faird/shared/code/external/envs/miniconda3/load_miniconda3.sh   # [FIX ME] MSI cluster faird group. Replace filepath with yours.
+    conda activate babs   # [FIX ME] replace 'babs' with your env variable name
+
+# Where to run the jobs:
+job_compute_space: "/tmp"   # [FIX ME] MSI cluster
+
+# Below is to filter out subjects (or sessions)
+#   right now we only filter based on unzipped dataset
+required_files:
+    $INPUT_DATASET_#1:
+        - "func/*_bold.nii*"
+        - "anat/*_T1w.nii*"
+
+# 'alert_log_messages': not to include this section for now.
diff --git a/notebooks/eg_fmriprepfake-0-1-2_legacy-layout_slurm_msi.yaml b/notebooks/eg_fmriprepfake-0-1-2_legacy-layout_slurm_msi.yaml
new file mode 100644
index 00000000..b60c21d3
--- /dev/null
+++ b/notebooks/eg_fmriprepfake-0-1-2_legacy-layout_slurm_msi.yaml
@@ -0,0 +1,52 @@
+# This is an example config yaml file for:
+#   BIDS App:         fmriprep-fake
+#   BIDS App version: 0.1.2
+#   Task:             `--output-layout legacy`, generating legacy output layout
+#   Which system:     Slurm
+#   Tested on which cluster:  UMN MSI cluster
+
+# Warning!!!
+#   This is only an example, which may not necessarily fit your purpose,
+#   or be an optimized solution for your case,
+#   or be compatible to the BIDS App version you're using.
+#   Therefore, please change and tailor it for your case before use it!!!
+
+# Arguments in `singularity run`:
+singularity_run:
+    --output-layout: "legacy"
+
+# Output foldername(s) to be zipped, and the BIDS App version to be included in the zip filename(s):
+#   For `--output-layout legacy`, users don't need to create the output folder,
+#   as all derivatives are in 'fmriprep' or 'freesurfer' folder.
+zip_foldernames:
+    fmriprep: "0-1-2"   # folder 'fmriprep' will be zipped into 'sub-xx_ses-yy_fmriprep-0-1-2.zip'
+    freesurfer: '0-1-2'   # folder 'freesurfer' will be zipped into 'sub-xx_ses-yy_freesurfer-0-1-2.zip'
+
+cluster_resources:
+    interpreting_shell: "/bin/bash -l"
+    hard_memory_limit: 2G
+    temporary_disk_space: 20G
+    hard_runtime_limit: "20"   # 20min
+    customized_text: |
+        #SBATCH -p amd2tb,ram256g
+# Notes: Above `customized_text` is MSI Slurm cluster specific.
+#   So it may not be relevant for other clusters
+
+# Users need to add their customized bash command below,
+#   they will be used as preambles in `participant_job.sh`
+#   the commands should not be quoted!
+script_preamble: |
+    source /home/faird/shared/code/external/envs/miniconda3/load_miniconda3.sh   # [FIX ME] MSI cluster faird group. Replace filepath with yours.
+    conda activate babs   # [FIX ME] replace 'babs' with your env variable name
+
+# Where to run the jobs:
+job_compute_space: "/tmp"   # [FIX ME] MSI cluster
+
+# Below is to filter out subjects (or sessions)
+#   right now we only filter based on unzipped dataset
+required_files:
+    $INPUT_DATASET_#1:
+        - "func/*_bold.nii*"
+        - "anat/*_T1w.nii*"
+
+# 'alert_log_messages': not to include this section for now.
diff --git a/notebooks/eg_qsiprep-0-16-0RC3_sloppy_sge_cubic.yaml b/notebooks/eg_qsiprep-0-16-0RC3_sloppy_sge_cubic.yaml
index 43e9ec53..2221731c 100644
--- a/notebooks/eg_qsiprep-0-16-0RC3_sloppy_sge_cubic.yaml
+++ b/notebooks/eg_qsiprep-0-16-0RC3_sloppy_sge_cubic.yaml
@@ -4,7 +4,6 @@
 #   Task:             `--sloppy` mode
 #   Which system:     SGE
 #   Tested on which cluster:  Penn Med CUBIC cluster
-# QSIPrep's Docker image is publicly available at: https://hub.docker.com/r/pennbbl/qsiprep
 
 # WARNING!!!
 #   This is only an example, which may not necessarily fit your purpose,
diff --git a/notebooks/eg_qsiprep-0-16-0RC3_sloppy_slurm_msi.yaml b/notebooks/eg_qsiprep-0-16-0RC3_sloppy_slurm_msi.yaml
index e292b7bf..737a6812 100644
--- a/notebooks/eg_qsiprep-0-16-0RC3_sloppy_slurm_msi.yaml
+++ b/notebooks/eg_qsiprep-0-16-0RC3_sloppy_slurm_msi.yaml
@@ -4,7 +4,6 @@
 #   Task:             `--sloppy` mode
 #   Which system:     Slurm
 #   Tested on which cluster:  MSI cluster
-# QSIPrep's Docker image is publicly available at: https://hub.docker.com/r/pennbbl/qsiprep
 
 # WARNING!!!
 #   This is only an example, which may not necessarily fit your purpose,
@@ -41,8 +40,7 @@ cluster_resources:
     number_of_cpus: "6"    # --> "#SBATCH --cpus-per-task=6"
     hard_runtime_limit: "48:00:00"    # --> "--time=48:00:00", i.e., 2 days. Should NOT large than partition's time limit!
     customized_text: |
-        #SBATCH -p ram256g
-# Other choices of job partitions on MSI: amd2tb,ram256g,v100,k40
+        #SBATCH -p amd2tb,ram256g
 # Notes: Above `customized_text` is MSI Slurm cluster specific.
 #   So it may not be relevant for other clusters
 
diff --git a/notebooks/eg_toybidsapp-0-0-7_zipped_slurm_msi.yaml b/notebooks/eg_toybidsapp-0-0-7_zipped_slurm_msi.yaml
new file mode 100644
index 00000000..ef742389
--- /dev/null
+++ b/notebooks/eg_toybidsapp-0-0-7_zipped_slurm_msi.yaml
@@ -0,0 +1,44 @@
+# This is an example config yaml file for:
+#   BIDS App:         toy BIDS App "toy_bids_app"
+#   BIDS App version: 0.0.7
+#   Task:             `--zipped`, for application to zipped BIDS derivatives dataset
+#   Which system:     Slurm
+#   Tested on which cluster:  UMN MSI cluster
+
+# Warning!!!
+#   This is only an example, which may not necessarily fit your purpose,
+#   or be an optimized solution for your case,
+#   or be compatible to the BIDS App version you're using.
+#   Therefore, please change and tailor it for your case before use it!!!
+
+# Arguments in `singularity run`:
+singularity_run:
+    --zipped: ""    # for zipped input dataset
+    --dummy: "2"   # this is a dummy variable, accepting values
+    -v: ""    # this is also a dummy variable, not accepting values
+
+# Output foldername(s) to be zipped, and the BIDS App version to be included in the zip filename(s):
+zip_foldernames:
+    toybidsapp: "0-0-7"   # folder 'toybidsapp' will be zipped into 'sub-xx_(ses-yy_)toybidsapp-0-0-7.zip'
+
+cluster_resources:
+    interpreting_shell: "/bin/bash -l"
+    hard_memory_limit: 25G
+    temporary_disk_space: 50G
+    hard_runtime_limit: "20"   # 20min
+    customized_text: |
+        #SBATCH -p amd2tb,ram256g
+# Notes: Above `customized_text` is MSI Slurm cluster specific.
+#   So it may not be relevant for other clusters
+
+# Necessary commands to be run first:
+script_preamble: |
+    source /home/faird/shared/code/external/envs/miniconda3/load_miniconda3.sh   # [FIX ME] MSI cluster faird group. Replace filepath with yours.
+    conda activate babs   # [FIX ME] replace 'babs' with your env variable name
+
+# Where to run the jobs:
+job_compute_space: "/tmp"   # [FIX ME] MSI cluster
+
+# 'required_files' section is not needed for toy BIDS App.
+
+# 'alert_log_messages' section is usually not needed for toy BIDS App.
diff --git a/notebooks/eg_xcpd-0-4-0_nifti_sge_cubic.yaml b/notebooks/eg_xcpd-0-4-0_nifti_sge_cubic.yaml
new file mode 100644
index 00000000..b510cca8
--- /dev/null
+++ b/notebooks/eg_xcpd-0-4-0_nifti_sge_cubic.yaml
@@ -0,0 +1,47 @@
+# This is an example config yaml file for:
+#   BIDS App:         XCP-D ("xcpd")
+#   BIDS App version: 0.4.0
+#   Task:             Running the entire workflow, for NIfTI images (i.e., without `--cifti`)
+#   Which system:     SGE
+#   Tested on which cluster:  PennMed CUBIC cluster
+
+# WARNING!!!
+#   This is only an example, which may not necessarily fit your purpose,
+#   or be an optimized solution for your case,
+#   or be compatible to the BIDS App version you're using.
+#   Therefore, please change and tailor it for your case before use it!!!
+
+# Arguments in `singularity run`:
+singularity_run:
+    -w: "$BABS_TMPDIR"   # this is a placeholder recognized BABS.
+    --despike: ""
+    --lower-bpf: "0.01"
+    --upper-bpf: "0.08"
+    -p: "36P"
+    --fd-thresh: "0.3"
+    -vvv: ""
+
+# Output foldername(s) to be zipped, and the BIDS App version to be included in the zip filename(s):
+#   XCP-D will automatically generate a folder called 'xcp_d' that wrap all the output files.
+zip_foldernames:
+    xcp_d: "0-4-0"     # folder 'xcp_d' will be zipped into 'sub-xx_(ses-yy_)xcp_d-0-4-0.zip'
+
+cluster_resources:
+    interpreting_shell: /bin/bash
+    hard_memory_limit: 32G
+    temporary_disk_space: 100G
+    hard_runtime_limit: "24:00:00"
+    customized_text: |
+        #$ -R y
+        #$ -l hostname=!compute-fed*
+# Notes: Above `customized_text` is Penn Med CUBIC cluster specific.
+#   So it's probably not relevant for other clusters
+
+# Necessary commands to be run first:
+script_preamble: |
+    source ${CONDA_PREFIX}/bin/activate mydatalad    # Penn Med CUBIC cluster; replace 'mydatalad' with your conda env name
+
+# Where to run the jobs:
+job_compute_space: "${CBICA_TMPDIR}"   # Penn Med CUBIC cluster tmp space
+
+# `required_files` and `alert_log_messages` sections are not provided in this example.
diff --git a/notebooks/show_babs_init_InputBIDS.ipynb b/notebooks/show_babs_init_InputBIDS.ipynb
index aa6d1b9b..0a8c5ba7 100644
--- a/notebooks/show_babs_init_InputBIDS.ipynb
+++ b/notebooks/show_babs_init_InputBIDS.ipynb
@@ -28,7 +28,8 @@
                 "InteractiveShell.ast_node_interactivity = 'all'   # print all outputs\n",
                 "\n",
                 "import os\n",
-                "import os.path as op"
+                "import os.path as op\n",
+                "import warnings"
             ]
         },
         {
@@ -47,7 +48,7 @@
                     "name": "stdout",
                     "output_type": "stream",
                     "text": [
-                        "/cbica/projects/BABS/babs/notebooks/eg_qsiprep-0-16-0RC3_sloppy_sge_cubic.yaml\n"
+                        "/cbica/projects/BABS/babs/notebooks/eg_fmriprep-23-1-3_sloppy_sge_cubic.yaml\n"
                     ]
                 }
             ],
@@ -55,10 +56,23 @@
                 "# This notebook only accepts toybidsapp_rawBIDS, qsiprep or fmriprep\n",
                 "#   or fmriprep_anatonly or 'fmriprep_sloppyFlag' or fmriprepfake (input ds: BIDS)\n",
                 "# ++++++++++++++++++++++++++++++++++\n",
-                "bidsapp = \"qsiprep\"\n",
-                "task_name = \"sloppy\"   # for fmriprep: 'anatonly', 'sloppy'; for toybidsapp: 'rawBIDS'\n",
+                "bidsapp = \"fmriprep\"\n",
+                "bidsapp_version_dash = \"23-1-3\"\n",
+                "# fmriprep: '20-2-3'; '23-1-3'\n",
+                "# qsiprep: '0-16-0RC3'\n",
+                "# toybidsapp: '0-0-7'\n",
+                "# fmirprep-fake: '0-1-2'\n",
+                "task_name = \"sloppy\"\n",
+                "# for fmriprep: 'anatonly', 'sloppy';\n",
+                "# for toybidsapp: 'rawBIDS', 'zipped'\n",
+                "# for fmriprep-fake: 'full' or 'legacy-layout' or 'anatonly'\n",
+                "input_ds_name = None\n",
+                "# `None` if task_name is not 'zipped'; \"fmriprep_anat\" for zip files from anat workflow\n",
+                "\n",
                 "type_session = \"multi-ses\"\n",
-                "which_dataset = \"toy_real\"    # \"toy_fake\", \"toy_real\", \"HBN\", \"PNC\"\n",
+                "which_dataset = \"toy_real\"    # \"toy_fake\", \"toy_real\", \"HBN\", \"PNC\", \"CCNP\", \"customize\"\n",
+                "input_ds = None    # None\n",
+                "# ^^ `None`` if `which_dataset` not 'customize'; please provide the path if `which_dataset` is 'customize'\n",
                 "\n",
                 "flag_where = \"cubic\"     # \"cubic\" or \"local\" or \"msi\"\n",
                 "type_system = \"sge\"   # \"sge\" or \"slurm\"\n",
@@ -87,7 +101,10 @@
                 "    raise Exception(\"not valid `flag_where`!\")\n",
                 "\n",
                 "# Input dataset:\n",
-                "if which_dataset == \"toy_fake\":\n",
+                "if which_dataset == \"customize\":\n",
+                "    assert (input_ds is not None)\n",
+                "    pass    # just use `input_ds` provided\n",
+                "elif which_dataset == \"toy_fake\":\n",
                 "    if type_session == \"multi-ses\":\n",
                 "        input_ds = \"https://osf.io/w2nu3/\"\n",
                 "        # input_ds = op.join(where_project, \"w2nu3\")\n",
@@ -108,27 +125,42 @@
                 "        input_ds = \"/home/faird/zhaoc/data/HBN_BIDS\"\n",
                 "elif which_dataset == \"PNC\":   # PNC data:\n",
                 "    assert type_session == \"single-ses\"\n",
-                "    input_ds = \"/home/faird/zhaoc/data/PNC_BIDS\"  # cloned from RBC github account\n",
+                "    input_ds = \"/home/faird/zhaoc/data/PNC_BIDS\"  # cloned from RBC github org\n",
+                "elif which_dataset == \"CCNP\":\n",
+                "    assert type_session == \"single-ses\"\n",
+                "    input_ds = \"/home/faird/zhaoc/data/CCNP_BIDS\"   # cloned from RBC github org\n",
                 "\n",
                 "\n",
                 "project_name = \"test_babs_\" + type_session\n",
                 "# Based on which dataset:\n",
-                "if which_dataset in [\"HBN\", \"PNC\"]:   # specific real dataset\n",
+                "if which_dataset in [\"HBN\", \"PNC\", \"CCNP\", \"customize\"]:   # specific real dataset\n",
                 "    project_name += \"_\" + which_dataset\n",
                 "# Based on which BIDS App:\n",
                 "if bidsapp == \"toybidsapp\":\n",
-                "    input_cli = [[\"BIDS\", input_ds]]\n",
-                "    container_name = bidsapp + \"-0-0-7\"\n",
+                "    container_name = bidsapp + \"-\" + bidsapp_version_dash\n",
+                "    if \"rawBIDS\" in task_name:\n",
+                "        input_ds_name = \"BIDS\"\n",
+                "    elif \"zipped\" in task_name:\n",
+                "        if input_ds_name is not None:\n",
+                "            pass   # just use whatever provided\n",
+                "        else:\n",
+                "            input_ds_name = \"zipped\"\n",
                 "elif bidsapp in [\"fmriprep\", \"fmriprep_anatonly\", \"fmriprep_sloppy\"]:\n",
-                "    container_name = bidsapp + \"-20-2-3\"\n",
+                "    container_name = bidsapp + \"-\" + bidsapp_version_dash\n",
                 "elif bidsapp == \"qsiprep\":\n",
-                "    container_name = bidsapp + \"-0-16-0RC3\"\n",
+                "    container_name = bidsapp + \"-\" + bidsapp_version_dash\n",
                 "elif bidsapp == \"fmriprepfake\":\n",
-                "    container_name = bidsapp + \"-0-1-1\"\n",
+                "    container_name = bidsapp + \"-\" + bidsapp_version_dash\n",
                 "else:\n",
                 "    raise Exception(\"Invalid `flag_instance`!\")\n",
                 "\n",
-                "project_name += \"_\" + bidsapp + \"_\" + task_name\n",
+                "if input_ds_name is None:\n",
+                "    input_ds_name = \"BIDS\"\n",
+                "\n",
+                "if \"fmriprep\" in bidsapp:\n",
+                "    project_name += \"_\" + bidsapp + \"-\" + bidsapp_version_dash + \"_\" + task_name\n",
+                "else:\n",
+                "    project_name += \"_\" + bidsapp + \"_\" + task_name\n",
                 "\n",
                 "\n",
                 "# Container:\n",
@@ -174,11 +206,11 @@
                         "The command to execute:\n",
                         "babs-init \\\n",
                         "\t--where_project /cbica/projects/BABS/data \\\n",
-                        "\t--project_name test_babs_multi-ses_qsiprep_sloppy \\\n",
+                        "\t--project_name test_babs_multi-ses_fmriprep-23-1-3_sloppy \\\n",
                         "\t--input BIDS /cbica/projects/BABS/data/testdata_NKI/data_hashedID_bids \\\n",
-                        "\t--container_ds /cbica/projects/BABS/data/qsiprep-container \\\n",
-                        "\t--container_name qsiprep-0-16-0RC3 \\\n",
-                        "\t--container_config_yaml_file /cbica/projects/BABS/babs/notebooks/eg_qsiprep-0-16-0RC3_sloppy_sge_cubic.yaml \\\n",
+                        "\t--container_ds /cbica/projects/BABS/data/fmriprep-container \\\n",
+                        "\t--container_name fmriprep-23-1-3 \\\n",
+                        "\t--container_config_yaml_file /cbica/projects/BABS/babs/notebooks/eg_fmriprep-23-1-3_sloppy_sge_cubic.yaml \\\n",
                         "\t--type_session multi-ses \\\n",
                         "\t--type_system sge\n",
                         "WARNING: make sure you've changed `--fs-license-file` value in YAML file if you use it!!!\n"
@@ -189,7 +221,7 @@
                 "cmd = \"babs-init \\\\\\n\"\n",
                 "cmd += \"\\t\" + \"--where_project \" + where_project + \" \\\\\\n\"\n",
                 "cmd += \"\\t\" + \"--project_name \" + project_name + \" \\\\\\n\"\n",
-                "cmd += \"\\t\" + \"--input \" + \"BIDS\" + \" \" + input_ds + \" \\\\\\n\"\n",
+                "cmd += \"\\t\" + \"--input \" + input_ds_name + \" \" + input_ds + \" \\\\\\n\"\n",
                 "if list_sub_file is not None:\n",
                 "    cmd += \"\\t\" + \"--list_sub_file \" + list_sub_file + \" \\\\\\n\"\n",
                 "cmd += \"\\t\" + \"--container_ds \" + container_ds + \" \\\\\\n\"\n",
diff --git a/notebooks/show_babs_init_fpfsin.ipynb b/notebooks/show_babs_init_fpfsin.ipynb
index 7137e3bb..007a1de3 100644
--- a/notebooks/show_babs_init_fpfsin.ipynb
+++ b/notebooks/show_babs_init_fpfsin.ipynb
@@ -40,35 +40,115 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 10,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "/cbica/projects/BABS/babs/notebooks/eg_fmriprep-20-2-3_ingressed-fs-sloppy_sge_cubic.yaml\n"
+     ]
+    }
+   ],
    "source": [
     "# This notebook only accepts fmriprep with freesurfer ingressed\n",
     "# ++++++++++++++++++++++++++++++++++\n",
-    "flag_instance = \"fmriprep_ingressed_fs\"\n",
-    "type_session = \"multi-ses\"\n",
+    "bidsapp = \"fmriprep\"\n",
+    "bidsapp_version_dash = \"20-2-3\"\n",
+    "# fmriprep: '20-2-3'; '23-1-3'\n",
+    "task_name = \"ingressed-fs-sloppy\"\n",
+    "\n",
+    "input_ds_name_fs = \"freesurfer\"\n",
+    "# zip files from anat workflow:\n",
+    "# e.g., \"fmriprep_anat\" for fmriprep 23.1.3; \"freesurfer\" for fmriprep 20.2.3\n",
+    "\n",
+    "type_session = \"single-ses\"\n",
+    "which_dataset = \"HBN\"    # \"toy_fake\", \"toy_real\", \"CCNP\", \"HBN\"\n",
+    "input_ds_fs = \"/cbica/projects/BABS/data/HBN_fmriprep_anat\"\n",
+    "# ^^ path to the fmriprep `--anat-only` cloned output ria \n",
+    "\n",
+    "flag_where = \"cubic\"     # \"cubic\" or \"local\" or \"msi\"\n",
+    "type_system = \"sge\"   # \"sge\" or \"slurm\"\n",
     "# ++++++++++++++++++++++++++++++++++\n",
-    "where_project = \"/Users/chenyzh/Desktop/Research/Satterthwaite_Lab/datalad_wrapper/data\"\n",
-    "where_notebooks = \"/Users/chenyzh/Desktop/Research/Satterthwaite_Lab/datalad_wrapper/babs/notebooks\"\n",
     "\n",
-    "if flag_instance == \"fmriprep_ingressed_fs\":\n",
-    "    project_name = \"test_babs_\" + type_session + \"_fpfsin\"\n",
-    "    bidsapp = \"fmriprep\"\n",
+    "# sanity checks:\n",
+    "if flag_where == \"cubic\":\n",
+    "    assert type_system == \"sge\"\n",
+    "elif flag_where == \"msi\":\n",
+    "    assert type_system == \"slurm\"\n",
+    "\n",
+    "# where:\n",
+    "if flag_where == \"cubic\":\n",
+    "    where_root = \"/cbica/projects/BABS\"\n",
+    "    where_project = op.join(where_root, \"data\")\n",
+    "    where_notebooks = op.join(where_root, \"babs/notebooks\")\n",
+    "elif flag_where == \"local\":\n",
+    "    where_root = \"/Users/chenyzh/Desktop/Research/Satterthwaite_Lab/datalad_wrapper\"\n",
+    "    where_project = op.join(where_root, \"data\")\n",
+    "    where_notebooks = op.join(where_root, \"babs/notebooks\")\n",
+    "elif flag_where == \"msi\":\n",
+    "    where_root = \"/home/faird/zhaoc\"\n",
+    "    where_project = \"/home/faird/zhaoc/data\"\n",
+    "    where_notebooks = op.join(where_root, \"babs/notebooks\")\n",
+    "else:\n",
+    "    raise Exception(\"not valid `flag_where`!\")\n",
+    "\n",
+    "# Input dataset:\n",
+    "if which_dataset == \"CCNP\":\n",
+    "    assert type_session == \"single-ses\"\n",
+    "    input_ds_bids = \"/home/faird/zhaoc/data/CCNP_BIDS\"   # cloned from RBC github org\n",
+    "elif which_dataset == \"HBN\":\n",
+    "    assert type_session == \"single-ses\"\n",
+    "    input_ds_bids = \"/cbica/projects/BABS/data/HBN_BIDS\"\n",
+    "elif which_dataset == \"toy_fake\":\n",
     "    if type_session == \"multi-ses\":\n",
     "        input_ds_bids = op.join(where_project, \"w2nu3\")  # bids, multi-ses\n",
     "        input_ds_fs = op.join(where_project, \"k9zw2\")   # fmriprep done, multi-ses\n",
     "    elif type_session == \"single-ses\":\n",
     "        input_ds_bids = op.join(where_project, \"t8urc\")   # bids, single-ses\n",
     "        input_ds_fs = \"osf://2jvub/\"   # fmriprep done, single-ses\n",
+    "elif which_dataset == \"toy_real\":\n",
+    "    if type_session == \"multi-ses\":\n",
+    "        # input_ds_bids = \"/cbica/projects/RBC/chenying_practice/data_for_babs/NKI/data_hashedID_bids\"\n",
+    "        input_ds_bids = \"/cbica/projects/BABS/data/testdata_NKI/data_hashedID_bids\"\n",
+    "    elif type_session == \"single-ses\":\n",
+    "        raise Exception(\"not supported yet!\")\n",
     "else:\n",
-    "    raise Exception(\"`flag_instance` is not 'fmriprep_ingressed_fs'!\")\n",
+    "    raise Exception(\"not valid `which_dataset`!\")\n",
+    "\n",
+    "assert \"ingressed-fs\" in task_name\n",
     "\n",
-    "container_ds = op.join(where_project, \"toybidsapp-container-docker\")\n",
-    "container_name = bidsapp + \"-0-0-0\"  # \"toybidsapp-0-0-3\"\n",
-    "container_config_yaml_file = op.join(where_notebooks, \"example_container_\" + flag_instance + \".yaml\")\n",
+    "bidsapp = \"fmriprep\"\n",
+    "container_name = \"fmriprep\" + \"-\" + bidsapp_version_dash\n",
     "\n",
-    "list_sub_file = op.join(where_notebooks, \"initial_sub_list_\" + type_session + \".csv\")"
+    "project_name = \"test_babs_\" + type_session\n",
+    "# Based on which dataset:\n",
+    "if which_dataset in [\"HBN\", \"PNC\", \"CCNP\", \"customize\"]:   # specific real dataset\n",
+    "    project_name += \"_\" + which_dataset\n",
+    "project_name += \"_\" + bidsapp + \"-\" + bidsapp_version_dash +  \"_\" + task_name\n",
+    "\n",
+    "# Container:\n",
+    "container_ds = op.join(where_project, bidsapp + \"-container\")  \n",
+    "if flag_where == \"local\":\n",
+    "    # container_ds += \"-docker\"   # add \"docker\" at the end\n",
+    "    container_ds = op.join(where_project, \"toybidsapp-container-docker\")\n",
+    "\n",
+    "container_config_yaml_file = op.join(where_notebooks, \"eg_\" + container_name\n",
+    "    + \"_\" + task_name + \"_\" + type_system)\n",
+    "if flag_where in [\"cubic\", \"msi\"]:\n",
+    "    container_config_yaml_file += \"_\" + flag_where\n",
+    "else:\n",
+    "    if type_system == \"sge\":\n",
+    "        container_config_yaml_file += \"_\" + \"cubic\"\n",
+    "    elif type_system == \"slurm\":\n",
+    "        container_config_yaml_file += \"_\" + \"msi\"\n",
+    "container_config_yaml_file += \".yaml\"\n",
+    "print(container_config_yaml_file)\n",
+    "assert op.exists(container_config_yaml_file)\n",
+    "\n",
+    "# list_sub_file = op.join(where_notebooks, \"initial_sub_list_\" + type_session + \".csv\")\n",
+    "list_sub_file = None"
    ]
   },
   {
@@ -80,93 +160,45 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "DataLad version: 0.17.2\n",
-      "nothing to save, working tree clean\n",
-      "nothing to save, working tree clean\n",
-      "\n",
-      "project_root of this BABS project: /Users/chenyzh/Desktop/Research/Satterthwaite_Lab/datalad_wrapper/data/test_babs_multi-ses_fpfsin\n",
-      "type of data of this BABS project: multi-ses\n",
-      "job scheduling system of this BABS project: sge\n",
-      "\n",
-      "\n",
-      "Creating `analysis` folder (also a datalad dataset)...\n",
-      "\u001b[1;31muntracked\u001b[0m: .gitignore (\u001b[1;35mfile\u001b[0m)\n",
-      "Folder 'analysis' exists in the `project_root` and is a datalad dataset; not to re-create it.\n",
-      "\n",
-      "Creating output and input RIA...\n",
-      "\n",
-      "Registering the input dataset(s)...\n",
-      "The input dataset #1 'BIDS' has been copied into `analysis` folder; not to copy again.\n",
-      "The input dataset #2 'freesurfer' has been copied into `analysis` folder; not to copy again.\n",
-      "\n",
-      "Checking whether each input dataset is a zipped or unzipped dataset...\n",
-      "input dataset 'BIDS' is considered as an unzipped dataset.\n",
-      "input dataset 'freesurfer' is considered as a zipped dataset.\n",
-      "Performing sanity check for any zipped input dataset... Getting example zip file(s) to check...\n",
-      "\u001b[1;1mget\u001b[0m(\u001b[1;32mok\u001b[0m): sub-01_ses-A_freesurfer-20.2.3.zip (\u001b[1;35mfile\u001b[0m) [from osf-storage...]\n",
-      "\u001b[1;1mdrop\u001b[0m(\u001b[1;32mok\u001b[0m): sub-01_ses-A_freesurfer-20.2.3.zip (\u001b[1;35mfile\u001b[0m)\n",
-      "Performing sanity check for any unzipped input dataset...\n",
-      "\n",
-      "Adding the container as a sub-dataset of `analysis` dataset...\n",
-      "The container has been added as a sub-dataset; not to do it again.\n",
-      "\n",
-      "Generating a bash script for running container and zipping the outputs...\n",
-      "This bash script will be named as `fmriprep-0-0-0_zip.sh`\n",
-      "\n",
-      "/Users/chenyzh/Desktop/Research/Satterthwaite_Lab/datalad_wrapper/babs/babs/utils.py:316: UserWarning: Usually BIDS App depends on TemplateFlow, but environment variable `TEMPLATEFLOW_HOME` was not set up. Therefore, BABS will not export it or bind its directory when running the container. This may cause errors.\n",
-      "  warnings.warn(\"Usually BIDS App depends on TemplateFlow,\"\n",
-      "Below is the generated `singularity run` command:\n",
-      "singularity run --cleanenv -B ${PWD} \\\n",
-      "\tcontainers/.datalad/environments/fmriprep-0-0-0/image \\\n",
-      "\tinputs/data/BIDS \\\n",
-      "\toutputs \\\n",
-      "\tparticipant \\\n",
-      "\t-w ${PWD}/.git/tmp/wkdir \\\n",
-      "\t--n_cpus 1 \\\n",
-      "\t--stop-on-first-crash \\\n",
-      "\t--fs-license-file code/license.txt \\\n",
-      "\t--skip-bids-validation \\\n",
-      "\t--output-spaces MNI152NLin6Asym:res-2 \\\n",
-      "\t--force-bbr \\\n",
-      "\t--cifti-output 91k \\\n",
-      "\t-v -v \\\n",
-      "\t--fs-subjects-dir inputs/data/freesurfer/freesurfer \\\n",
-      "\t--bids-filter-file \"${filterfile}\" \\\n",
-      "\t--participant-label \"${subid}\"\n",
-      "Traceback (most recent call last):\n",
-      "  File \"/Users/chenyzh/opt/miniconda3/envs/mydatalad/bin/babs-init\", line 33, in <module>\n",
-      "    sys.exit(load_entry_point('BABS', 'console_scripts', 'babs-init')())\n",
-      "  File \"/Users/chenyzh/Desktop/Research/Satterthwaite_Lab/datalad_wrapper/babs/babs/cli.py\", line 80, in babs_init_cli\n",
-      "    babs_init(args.where_project, args.project_name,\n",
-      "  File \"/Users/chenyzh/Desktop/Research/Satterthwaite_Lab/datalad_wrapper/babs/babs/core_functions.py\", line 84, in babs_init\n",
-      "    babs_proj.babs_bootstrap(input_ds, container_ds, container_name, container_config_yaml_file,\n",
-      "  File \"/Users/chenyzh/Desktop/Research/Satterthwaite_Lab/datalad_wrapper/babs/babs/babs.py\", line 335, in babs_bootstrap\n",
-      "    container.generate_bash_run_bidsapp(bash_path, input_ds, self.type_session)\n",
-      "  File \"/Users/chenyzh/Desktop/Research/Satterthwaite_Lab/datalad_wrapper/babs/babs/babs.py\", line 881, in generate_bash_run_bidsapp\n",
-      "    raise Exception(\n",
-      "Exception: FreeSurfer's license will be used but `$FREESURFER_HOME` was not set. Therefore, BABS cannot copy and paste FreeSurfer's license...\n"
+      "# The command to execute:\n",
+      "babs-init \\\n",
+      "\t--where_project /cbica/projects/BABS/data \\\n",
+      "\t--project_name test_babs_single-ses_HBN_fmriprep-20-2-3_ingressed-fs-sloppy \\\n",
+      "\t--input BIDS /cbica/projects/BABS/data/HBN_BIDS \\\n",
+      "\t--input freesurfer /cbica/projects/BABS/data/HBN_fmriprep_anat \\\n",
+      "\t--container_ds /cbica/projects/BABS/data/fmriprep-container \\\n",
+      "\t--container_name fmriprep-20-2-3 \\\n",
+      "\t--container_config_yaml_file /cbica/projects/BABS/babs/notebooks/eg_fmriprep-20-2-3_ingressed-fs-sloppy_sge_cubic.yaml \\\n",
+      "\t--type_session single-ses \\\n",
+      "\t--type_system sge\n",
+      "WARNING: make sure you've changed `--fs-license-file` value in YAML file if you use it!!!\n"
      ]
     }
    ],
    "source": [
-    "!(babs-init \\\n",
-    "    --where_project $where_project \\\n",
-    "    --project_name $project_name \\\n",
-    "    --input \"BIDS\" $input_ds_bids \\\n",
-    "    --input \"freesurfer\" $input_ds_fs \\\n",
-    "    --list_sub_file $list_sub_file \\\n",
-    "    --container_ds $container_ds \\\n",
-    "    --container_name $container_name \\\n",
-    "    --container_config_yaml_file $container_config_yaml_file \\\n",
-    "    --type_session $type_session \\\n",
-    "    --type_system sge)"
+    "cmd = \"babs-init \\\\\\n\"\n",
+    "cmd += \"\\t\" + \"--where_project \" + where_project + \" \\\\\\n\"\n",
+    "cmd += \"\\t\" + \"--project_name \" + project_name + \" \\\\\\n\"\n",
+    "cmd += \"\\t\" + \"--input \" + \"BIDS\" + \" \" + input_ds_bids + \" \\\\\\n\"\n",
+    "cmd += \"\\t\" + \"--input \" + input_ds_name_fs + \" \" + input_ds_fs + \" \\\\\\n\"\n",
+    "if list_sub_file is not None:\n",
+    "    cmd += \"\\t\" + \"--list_sub_file \" + list_sub_file + \" \\\\\\n\"\n",
+    "cmd += \"\\t\" + \"--container_ds \" + container_ds + \" \\\\\\n\"\n",
+    "cmd += \"\\t\" + \"--container_name \" + container_name + \" \\\\\\n\"\n",
+    "cmd += \"\\t\" + \"--container_config_yaml_file \" + container_config_yaml_file + \" \\\\\\n\"\n",
+    "cmd += \"\\t\" + \"--type_session \" + type_session + \" \\\\\\n\"\n",
+    "cmd += \"\\t\" + \"--type_system \" + type_system\n",
+    "\n",
+    "print(\"# The command to execute:\")\n",
+    "print(cmd)\n",
+    "print(\"WARNING: make sure you've changed `--fs-license-file` value in YAML file if you use it!!!\")"
    ]
   }
  ],
@@ -186,7 +218,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:58:50) \n[GCC 10.3.0]"
+   "version": "3.9.16"
   },
   "orig_nbformat": 4,
   "vscode": {
diff --git a/notebooks/show_babs_init_xcpd.ipynb b/notebooks/show_babs_init_xcpd.ipynb
new file mode 100644
index 00000000..faf98d30
--- /dev/null
+++ b/notebooks/show_babs_init_xcpd.ipynb
@@ -0,0 +1,229 @@
+{
+    "cells": [
+        {
+            "cell_type": "markdown",
+            "metadata": {},
+            "source": [
+                "This jupyter notebook is to show function `babs-init`."
+            ]
+        },
+        {
+            "cell_type": "code",
+            "execution_count": 1,
+            "metadata": {},
+            "outputs": [],
+            "source": [
+                "# See `README_howtorun_show_babs_init_ipynb.md` for how to run this file!\n",
+                "\n",
+                "# Clone out:\n",
+                "#   datalad clone ria+file:///path/to/<container>/output_ria#~data singleORmulti-ses_<container>_outputs\n",
+                "# If you want to change `project_root`'s foldername, also change `output_ria/alias/data` symlink:\n",
+                "    # cd output_ria/alias\n",
+                "    # ln -sf /new/full/path/to/output_ria/xxx/xxx-xxx-xxx-xxx data\n",
+                "\n",
+                "# flake8: noqa\n",
+                "\n",
+                "# set up how Jupyter notebook behaves:\n",
+                "from IPython.core.interactiveshell import InteractiveShell\n",
+                "InteractiveShell.ast_node_interactivity = 'all'   # print all outputs\n",
+                "\n",
+                "import os\n",
+                "import os.path as op\n",
+                "import warnings"
+            ]
+        },
+        {
+            "cell_type": "markdown",
+            "metadata": {},
+            "source": [
+                "There are several arguments when calling `babs-init`:"
+            ]
+        },
+        {
+            "cell_type": "code",
+            "execution_count": 3,
+            "metadata": {},
+            "outputs": [
+                {
+                    "name": "stdout",
+                    "output_type": "stream",
+                    "text": [
+                        "/cbica/projects/BABS/babs/notebooks/eg_xcpd-0-4-0_nifti_sge_cubic.yaml\n"
+                    ]
+                }
+            ],
+            "source": [
+                "# This notebook only accepts toybidsapp_rawBIDS, qsiprep or fmriprep\n",
+                "#   or fmriprep_anatonly or 'fmriprep_sloppyFlag' or fmriprepfake (input ds: BIDS)\n",
+                "# ++++++++++++++++++++++++++++++++++\n",
+                "bidsapp = \"xcpd\"\n",
+                "bidsapp_version_dash = \"0-4-0\"\n",
+                "# xcp-d: '0-3-0'; '0-4-0'\n",
+                "\n",
+                "# fmriprep_version_dash = \"22-0-2\"\n",
+                "# fmriprep output: '22-0-2' for HBN fmriprep func outputs; '20.2.3' for CCNP fmriprep outputs\n",
+                "\n",
+                "task_name = \"nifti\"    # \"nifti\"\n",
+                "\n",
+                "input_ds_name = \"fmriprep\"    # \"fmriprep\"\n",
+                "\n",
+                "type_session = \"single-ses\"\n",
+                "which_dataset = \"CCNP\"    # \"HBN\"\n",
+                "input_ds = None    # None\n",
+                "# ^^ `None`` if `which_dataset` not 'customize'; please provide the path if `which_dataset` is 'customize'\n",
+                "\n",
+                "flag_where = \"cubic\"     # \"cubic\" or \"local\" or \"msi\"\n",
+                "type_system = \"sge\"   # \"sge\" or \"slurm\"\n",
+                "# ++++++++++++++++++++++++++++++++++\n",
+                "\n",
+                "# sanity checks:\n",
+                "if flag_where == \"cubic\":\n",
+                "    assert type_system == \"sge\"\n",
+                "elif flag_where == \"msi\":\n",
+                "    assert type_system == \"slurm\"\n",
+                "\n",
+                "# where:\n",
+                "if flag_where == \"cubic\":\n",
+                "    where_root = \"/cbica/projects/BABS\"\n",
+                "    where_project = op.join(where_root, \"data\")\n",
+                "    where_notebooks = op.join(where_root, \"babs/notebooks\")\n",
+                "elif flag_where == \"local\":\n",
+                "    where_root = \"/Users/chenyzh/Desktop/Research/Satterthwaite_Lab/datalad_wrapper\"\n",
+                "    where_project = op.join(where_root, \"data\")\n",
+                "    where_notebooks = op.join(where_root, \"babs/notebooks\")\n",
+                "elif flag_where == \"msi\":\n",
+                "    where_root = \"/home/faird/zhaoc\"\n",
+                "    where_project = \"/home/faird/zhaoc/data\"\n",
+                "    where_notebooks = op.join(where_root, \"babs/notebooks\")\n",
+                "else:\n",
+                "    raise Exception(\"not valid `flag_where`!\")\n",
+                "\n",
+                "# Input dataset:\n",
+                "if which_dataset == \"HBN\":  # HBN data:\n",
+                "    assert type_session == \"single-ses\"\n",
+                "    if flag_where == \"cubic\":\n",
+                "        input_ds = \"/cbica/projects/BABS/data/HBN_fmriprep_func\"  # datalad sibling in BABS cubic project\n",
+                "elif which_dataset == \"CCNP\":   # CCNP data:\n",
+                "    assert type_session == \"single-ses\"\n",
+                "    if flag_where == \"cubic\":\n",
+                "        input_ds = \"/cbica/projects/BABS/data/CCNP_fmriprep\"\n",
+                "project_name = \"test_babs_\" + type_session\n",
+                "# Based on which dataset:\n",
+                "if which_dataset in [\"HBN\", \"PNC\", \"CCNP\", \"customize\"]:   # specific real dataset\n",
+                "    project_name += \"_\" + which_dataset\n",
+                "# Based on which BIDS App:\n",
+                "assert bidsapp == \"xcpd\"\n",
+                "container_name = bidsapp + \"-\" + bidsapp_version_dash\n",
+                "\n",
+                "project_name += \"_\" + bidsapp + \"_\" + task_name\n",
+                "\n",
+                "# Container:\n",
+                "container_ds = op.join(where_project, bidsapp + \"-container\")  \n",
+                "if flag_where == \"local\":\n",
+                "    # container_ds += \"-docker\"   # add \"docker\" at the end\n",
+                "    container_ds = op.join(where_project, \"toybidsapp-container-docker\")\n",
+                "\n",
+                "container_config_yaml_file = op.join(where_notebooks, \"eg_\" + container_name\n",
+                "    + \"_\" + task_name + \"_\" + type_system)\n",
+                "if flag_where in [\"cubic\", \"msi\"]:\n",
+                "    container_config_yaml_file += \"_\" + flag_where\n",
+                "else:\n",
+                "    if type_system == \"sge\":\n",
+                "        container_config_yaml_file += \"_\" + \"cubic\"\n",
+                "    elif type_system == \"slurm\":\n",
+                "        container_config_yaml_file += \"_\" + \"msi\"\n",
+                "container_config_yaml_file += \".yaml\"\n",
+                "print(container_config_yaml_file)\n",
+                "assert op.exists(container_config_yaml_file)\n",
+                "# container_config_yaml_file = op.join(where_notebooks, \"example_container_\" + flag_instance + \".yaml\")\n",
+                "\n",
+                "# list_sub_file = op.join(where_notebooks, \"initial_sub_list_\" + type_session + \".csv\")\n",
+                "list_sub_file = None"
+            ]
+        },
+        {
+            "cell_type": "markdown",
+            "metadata": {},
+            "source": [
+                "Let's pass these arguments into `babs-init` CLI:"
+            ]
+        },
+        {
+            "cell_type": "code",
+            "execution_count": 4,
+            "metadata": {},
+            "outputs": [
+                {
+                    "name": "stdout",
+                    "output_type": "stream",
+                    "text": [
+                        "The command to execute:\n",
+                        "babs-init \\\n",
+                        "\t--where_project /cbica/projects/BABS/data \\\n",
+                        "\t--project_name test_babs_single-ses_CCNP_xcpd_nifti \\\n",
+                        "\t--input fmriprep /cbica/projects/BABS/data/CCNP_fmriprep \\\n",
+                        "\t--container_ds /cbica/projects/BABS/data/xcpd-container \\\n",
+                        "\t--container_name xcpd-0-4-0 \\\n",
+                        "\t--container_config_yaml_file /cbica/projects/BABS/babs/notebooks/eg_xcpd-0-4-0_nifti_sge_cubic.yaml \\\n",
+                        "\t--type_session single-ses \\\n",
+                        "\t--type_system sge\n",
+                        "WARNING: make sure you've changed `--fs-license-file` value in YAML file if you use it!!!\n"
+                    ]
+                }
+            ],
+            "source": [
+                "cmd = \"babs-init \\\\\\n\"\n",
+                "cmd += \"\\t\" + \"--where_project \" + where_project + \" \\\\\\n\"\n",
+                "cmd += \"\\t\" + \"--project_name \" + project_name + \" \\\\\\n\"\n",
+                "cmd += \"\\t\" + \"--input \" + input_ds_name + \" \" + input_ds + \" \\\\\\n\"\n",
+                "if list_sub_file is not None:\n",
+                "    cmd += \"\\t\" + \"--list_sub_file \" + list_sub_file + \" \\\\\\n\"\n",
+                "cmd += \"\\t\" + \"--container_ds \" + container_ds + \" \\\\\\n\"\n",
+                "cmd += \"\\t\" + \"--container_name \" + container_name + \" \\\\\\n\"\n",
+                "cmd += \"\\t\" + \"--container_config_yaml_file \" + container_config_yaml_file + \" \\\\\\n\"\n",
+                "cmd += \"\\t\" + \"--type_session \" + type_session + \" \\\\\\n\"\n",
+                "cmd += \"\\t\" + \"--type_system \" + type_system\n",
+                "\n",
+                "print(\"The command to execute:\")\n",
+                "print(cmd)\n",
+                "print(\"WARNING: make sure you've changed `--fs-license-file` value in YAML file if you use it!!!\")"
+            ]
+        },
+        {
+            "cell_type": "code",
+            "execution_count": null,
+            "metadata": {},
+            "outputs": [],
+            "source": [
+                "!($cmd)"
+            ]
+        }
+    ],
+    "metadata": {
+        "kernelspec": {
+            "display_name": "mydatalad",
+            "language": "python",
+            "name": "python3"
+        },
+        "language_info": {
+            "codemirror_mode": {
+                "name": "ipython",
+                "version": 3
+            },
+            "file_extension": ".py",
+            "mimetype": "text/x-python",
+            "name": "python",
+            "nbconvert_exporter": "python",
+            "pygments_lexer": "ipython3",
+            "version": "3.9.16 (main, Mar  8 2023, 14:00:05) \n[GCC 11.2.0]"
+        },
+        "orig_nbformat": 4,
+        "vscode": {
+            "interpreter": {
+                "hash": "abcc7813313a81f6f916a4574498d1c2de65ad7fdfeb04d04cdf237cdcbdda8b"
+            }
+        }
+    },
+    "nbformat": 4,
+    "nbformat_minor": 2
+}