rename yaml files for fmriprep/qsiprep; update comments

notebooks/example_container_fmriprep_sloppyFlag.yaml → notebooks/eg_fmriprep-20-2-3_sloppy_sge_cubic.yaml

@@ -1,37 +1,43 @@
-# This is an example config yaml file for fMRIPrep version 20.2.3,
-#   but in `--sloppy` mode, i.e., test mode, and there is no FreeSurfer recon either.
-# This should NOT be used to produce real outputs you need.
+# 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
+# fMRIPrep's Docker image is publicly available at: https://hub.docker.com/r/nipreps/fmriprep/
 
-# Warning!!!
+# 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 fMRIPrep version you're using.
+#   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`:
-# You should not have flags of : `--participant-label`, or `--bids-filter-file`!
 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"  # 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: Null  # Null or NULL is also a placeholder
-    --output-spaces: "MNI152NLin6Asym:res-2 MNI152NLin2009cAsym"   # e.g., two output spaces
+    --output-spaces: "MNI152NLin6Asym:res-2"   # for two output spaces: e.g., "MNI152NLin6Asym:res-2 MNI152NLin2009cAsym"
     --force-bbr: ""
-    #--cifti-output: 91k   # ADD THIS WHEN FULL RUN!
     -v: '-v'   # this is for double "-v"
-    --sloppy: ''      # TEST RUN!
-    --fs-no-reconall: ''   # TEST RUN!
+    --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   # "-S /bin/bash" on cubic
-    hard_memory_limit: 25G   # "-l h_vmem=25G" on cubic
-    temporary_disk_space: 200G   # "-l tmpfree=200G" on cubic  # this is highly-recommended on cubic
+    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*
@@ -42,16 +48,16 @@ cluster_resources:
 #   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.
+    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: "${CBICA_TMPDIR}"   # Penn Med CUBIC cluster tmp space
+job_compute_space: "${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

notebooks/eg_qsiprep-0-16-0RC3_sloppy_sge_cubic.yaml

@@ -0,0 +1,60 @@
+# This is an example config yaml file for:
+#   BIDS App:         QSIPrep ("qsiprep")
+#   BIDS App version: 0.16.0RC3
+#   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,
+#   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 QSIPrep.
+#   Therefore this YAML file should only be used for testing purpose.
+#   You should NOT use this YAML file to generate formal results!
+
+singularity_run:
+    -v: "-v"
+    -w: "$BABS_TMPDIR"   # this is a placeholder. To be changed to `${PWD}/.git/tmp/wkdir`
+    --n_cpus: "$NSLOTS"   # `$NSLOTS` can be recognized by SGE
+    --omp-nthreads: "3"   # without this, only run single-threaded jobs (N=`--n_cpus`) at once
+    --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
+    --unringing-method: "mrdegibbs"
+    --output-resolution: "2.0"
+    --sloppy: ""    # WARNING: only use this when testing
+    --hmc-model: "none"   # WARNING: only use this when testing
+    --dwi-only: ""   # WARNING: only use this when testing
+
+# Output foldername(s) to be zipped, and the BIDS App version to be included in the zip filename(s):
+zip_foldernames:
+    qsiprep: "0-16-0RC3"     # folder 'qsiprep' will be zipped into 'sub-xx_ses-yy_qsiprep-0-16-0RC3.zip'
+
+cluster_resources:
+    interpreting_shell: /bin/bash   # --> "#!/bin/bash"
+    hard_memory_limit: 32G   # --> `#$ -l h_vmem=32G`
+    temporary_disk_space: 200G   # --> `#$ -l tmpfree=200G`
+    number_of_cpus: "6"    # --> `#$ -pe threaded 6`
+    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 ${CONDA_PREFIX}/bin/activate mydatalad    # [FIX ME] Penn Med CUBIC cluster; replace 'mydatalad' with your conda env name
+    echo "I am running BABS."   # [FIX ME] this is an example command to show how to add another line; not necessary to include.
+
+# Where to run the jobs:
+job_compute_space: "${CBICA_TMPDIR}"   # [FIX ME] Penn Med CUBIC cluster tmp space
+
+required_files:
+    $INPUT_DATASET_#1:
+        - "dwi/*_dwi.nii*"   # QSIPrep

notebooks/eg_qsiprep-0-16-0RC3_sloppy_slurm_msi.yaml

@@ -35,7 +35,7 @@ zip_foldernames:
     qsiprep: "0-16-0RC3"     # folder 'qsiprep' will be zipped into 'sub-xx_ses-yy_qsiprep-0-16-0RC3.zip'
 
 cluster_resources:
-    interpreting_shell: "/bin/bash -l" # --> "#!/bin/bash -l"
+    interpreting_shell: "/bin/bash -l"   # --> "#!/bin/bash -l"
     hard_memory_limit: 32G   # --> "#SBATCH --mem=32G"
     temporary_disk_space: 200G   # --> "#SBATCH --tmp=200G"
     number_of_cpus: "6"    # --> "#SBATCH --cpus-per-task=6"

notebooks/show_babs_init_InputBIDS.ipynb

@@ -40,14 +40,14 @@
         },
         {
             "cell_type": "code",
-            "execution_count": 4,
+            "execution_count": 2,
             "metadata": {},
             "outputs": [
                 {
                     "name": "stdout",
                     "output_type": "stream",
                     "text": [
-                        "/home/faird/zhaoc/babs/notebooks/eg_qsiprep-0-16-0RC3_sloppy_slurm_msi.yaml\n"
+                        "/cbica/projects/BABS/babs/notebooks/eg_qsiprep-0-16-0RC3_sloppy_sge_cubic.yaml\n"
                     ]
                 }
             ],
@@ -57,11 +57,11 @@
                 "# ++++++++++++++++++++++++++++++++++\n",
                 "bidsapp = \"qsiprep\"\n",
                 "task_name = \"sloppy\"   # for fmriprep: 'anatonly', 'sloppy'; for toybidsapp: 'rawBIDS'\n",
-                "type_session = \"single-ses\"\n",
-                "which_dataset = \"HBN\"    # \"toy_fake\", \"toy_real\", \"HBN\", \"PNC\"\n",
+                "type_session = \"multi-ses\"\n",
+                "which_dataset = \"toy_real\"    # \"toy_fake\", \"toy_real\", \"HBN\", \"PNC\"\n",
                 "\n",
-                "flag_where = \"msi\"     # \"cubic\" or \"local\" or \"msi\"\n",
-                "type_system = \"slurm\"   # \"sge\" or \"slurm\"\n",
+                "flag_where = \"cubic\"     # \"cubic\" or \"local\" or \"msi\"\n",
+                "type_system = \"sge\"   # \"sge\" or \"slurm\"\n",
                 "# ++++++++++++++++++++++++++++++++++\n",
                 "\n",
                 "# sanity checks:\n",
@@ -164,7 +164,7 @@
         },
         {
             "cell_type": "code",
-            "execution_count": 5,
+            "execution_count": 3,
             "metadata": {},
             "outputs": [
                 {
@@ -173,14 +173,14 @@
                     "text": [
                         "The command to execute:\n",
                         "babs-init \\\n",
-                        "\t--where_project /home/faird/zhaoc/data \\\n",
-                        "\t--project_name test_babs_single-ses_HBN_qsiprep_sloppy \\\n",
-                        "\t--input BIDS /home/faird/zhaoc/data/HBN_BIDS \\\n",
-                        "\t--container_ds /home/faird/zhaoc/data/qsiprep-container \\\n",
+                        "\t--where_project /cbica/projects/BABS/data \\\n",
+                        "\t--project_name test_babs_multi-ses_qsiprep_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 /home/faird/zhaoc/babs/notebooks/eg_qsiprep-0-16-0RC3_sloppy_slurm_msi.yaml \\\n",
-                        "\t--type_session single-ses \\\n",
-                        "\t--type_system slurm\n",
+                        "\t--container_config_yaml_file /cbica/projects/BABS/babs/notebooks/eg_qsiprep-0-16-0RC3_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"
                     ]
                 }
@@ -215,7 +215,7 @@
     ],
     "metadata": {
         "kernelspec": {
-            "display_name": "babs",
+            "display_name": "mydatalad",
             "language": "python",
             "name": "python3"
         },
@@ -234,7 +234,7 @@
         "orig_nbformat": 4,
         "vscode": {
             "interpreter": {
-                "hash": "2538d15ebb217aff7ed13fa29cc6f5f706af190e6008d76f30d7ce8c1383d79a"
+                "hash": "abcc7813313a81f6f916a4574498d1c2de65ad7fdfeb04d04cdf237cdcbdda8b"
             }
         }
     },