Stop ingressing anatomical-space tissue segmentation file (PennLINC#1190

)

docs/outputs.rst

@@ -107,7 +107,7 @@ Atlases are written out to the ``atlases`` subfolder, following BEP038.
 Anatomical Outputs
 ******************
 
-Anatomical outputs consist of anatomical preprocessed T1w/T2w and segmentation images in MNI space.
+Anatomical outputs consist of anatomical preprocessed T1w and/or T2w images in MNI space.
 
 .. code-block::
 
@@ -116,7 +116,6 @@ Anatomical outputs consist of anatomical preprocessed T1w/T2w and segmentation i
          anat/
             <source_entities>_space-MNI152NLin6Asym_desc-preproc_T1w.nii.gz
             <source_entities>_space-MNI152NLin6Asym_desc-preproc_T2w.nii.gz
-            <source_entities>_space-MNI152NLin6Asym_dseg.nii.gz
 
 
 Surface mesh files

docs/usage.rst

@@ -169,9 +169,6 @@ We recommend NOT setting the datatype, suffix, or file extension in the filter f
 ``"t2w"`` selects a native T1w-space, preprocessed T2w file.
 If a T1w file is not available, this file will be in T2w space.
 
-``"anat_dseg"`` selects a segmentation file in the same space as the BOLD data.
-This file is not used for anything.
-
 ``"anat_brainmask"`` selects an anatomically-derived brain mask in the same space as the BOLD data.
 This file is used (1) to estimate head radius for FD calculation and
 (2) to calculate coregistration quality metrics.

docs/workflows.rst

@@ -872,8 +872,7 @@ Second, XCP-D outputs processed BOLD data, including denoised unsmoothed and smo
 MNI152NLin2009cAsym and fsLR-32k spaces, parcellated time series, functional connectivity matrices,
 and ALFF and ReHo (smoothed and unsmoothed).
 
-Third, the anatomical data (processed T1w processed and segmentation files) are copied from
-fMRIPrep.
+Third, the anatomical data (processed T1w and/or T2w files) are copied from fMRIPrep.
 If both images are not in MNI152NLin6Asym space, they are resampled to MNI space.
 The fMRIPrep surfaces (gifti files) in each subject are also resampled to standard space
 (fsLR-32K).

xcp_d/data/io_spec.yaml

@@ -6,16 +6,6 @@ queries:
             desc: brain
             extension: .nii.gz
             suffix: mask
-        # native anatomical-space dseg file
-        anat_dseg:
-            datatype: anat
-            desc: null
-            extension: .nii.gz
-            space:
-            - T1w
-            - T2w
-            - null
-            suffix: dseg
         # transform from native anatomical (T1w or T2w) space to same standard space as BOLD
         # "to" entity will be set later
         anat_to_template_xfm:

xcp_d/ingression/ukbiobank.py

@@ -238,13 +238,6 @@ def convert_ukb_to_bids_single_subject(in_dir, out_dir, sub_id, ses_id):
             f"{subses_ents}_space-{VOLSPACE}_desc-brain_mask.nii.gz",
         )
     )
-    # Use the brain mask as the "aparcaseg" dseg too.
-    copy_dictionary[warp_brainmask_to_std_results.outputs.out_file].append(
-        os.path.join(
-            anat_dir_bids,
-            f"{subses_ents}_space-{VOLSPACE}_desc-aparcaseg_dseg.nii.gz",
-        )
-    )
 
     # Warp the reference file to MNI space.
     warp_boldref_to_std = ApplyWarp(

xcp_d/ingression/utils.py

@@ -21,7 +21,6 @@ def collect_anatomical_files(anat_dir_orig, anat_dir_bids, base_anatomical_ents)
         "T1w.nii.gz": "desc-preproc_T1w.nii.gz",
         "brainmask_fs.nii.gz": "desc-brain_mask.nii.gz",
         "ribbon.nii.gz": "desc-ribbon_T1w.nii.gz",
-        "aparc+aseg.nii.gz": "desc-aparcaseg_dseg.nii.gz",
     }
     copy_dictionary = {}
 

xcp_d/interfaces/utils.py

@@ -64,13 +64,6 @@ class _ConvertTo32InputSpec(BaseInterfaceInputSpec):
         mandatory=False,
         usedefault=True,
     )
-    anat_dseg = traits.Either(
-        None,
-        File(exists=True),
-        desc="T1-space segmentation file",
-        mandatory=False,
-        usedefault=True,
-    )
 
 
 class _ConvertTo32OutputSpec(TraitedSpec):
@@ -104,12 +97,6 @@ class _ConvertTo32OutputSpec(TraitedSpec):
         desc="T2-weighted anatomical file",
         mandatory=False,
     )
-    anat_dseg = traits.Either(
-        None,
-        File(exists=True),
-        desc="T1-space segmentation file",
-        mandatory=False,
-    )
 
 
 class ConvertTo32(SimpleInterface):
@@ -124,7 +111,6 @@ def _run_interface(self, runtime):
         self._results["bold_mask"] = downcast_to_32(self.inputs.bold_mask)
         self._results["t1w"] = downcast_to_32(self.inputs.t1w)
         self._results["t2w"] = downcast_to_32(self.inputs.t2w)
-        self._results["anat_dseg"] = downcast_to_32(self.inputs.anat_dseg)
 
         return runtime
 

xcp_d/tests/conftest.py

@@ -122,7 +122,6 @@ def ds001419_data(datasets):
         anat_dir,
         "sub-01_space-MNI152NLin2009cAsym_res-2_desc-preproc_T1w.nii.gz",
     )
-    files["anat_dseg"] = os.path.join(anat_dir, "sub-01_desc-aseg_dseg.nii.gz")
 
     return files
 
@@ -182,10 +181,6 @@ def pnc_data(datasets):
             "res-2_desc-preproc_T1w.nii.gz"
         ),
     )
-    files["anat_dseg"] = os.path.join(
-        anat_dir,
-        "sub-1648798153_ses-PNC1_acq-refaced_desc-aseg_dseg.nii.gz",
-    )
 
     return files
 

xcp_d/tests/data/test_ds001419_cifti_outputs.txt

@@ -27,7 +27,6 @@ sub-01
 sub-01.html
 sub-01/anat
 sub-01/anat/sub-01_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz
-sub-01/anat/sub-01_space-MNI152NLin2009cAsym_dseg.nii.gz
 sub-01/func
 sub-01/func/sub-01_task-imagery_desc-abcc_qc.hdf5
 sub-01/func/sub-01_task-imagery_desc-filtered_motion.json

xcp_d/tests/data/test_ds001419_nifti_outputs.txt

@@ -9,7 +9,6 @@ sub-01
 sub-01.html
 sub-01/anat
 sub-01/anat/sub-01_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz
-sub-01/anat/sub-01_space-MNI152NLin2009cAsym_dseg.nii.gz
 sub-01/func
 sub-01/func/sub-01_task-imagery_desc-filtered_motion.json
 sub-01/func/sub-01_task-imagery_desc-filtered_motion.tsv

xcp_d/tests/data/test_fmriprep_without_freesurfer_outputs.txt

@@ -67,7 +67,6 @@ sub-01
 sub-01.html
 sub-01/anat
 sub-01/anat/sub-01_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz
-sub-01/anat/sub-01_space-MNI152NLin2009cAsym_dseg.nii.gz
 sub-01/func
 sub-01/func/sub-01_task-mixedgamblestask_run-1_desc-abcc_qc.hdf5
 sub-01/func/sub-01_task-mixedgamblestask_run-1_desc-preproc_design.json

xcp_d/tests/data/test_nibabies_outputs.txt

@@ -67,7 +67,6 @@ sub-01.html
 sub-01/ses-1mo
 sub-01/ses-1mo/anat
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_desc-preproc_T1w.nii.gz
-sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-MNIInfant_cohort-1_dseg.nii.gz
 sub-01/ses-1mo/func
 sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_desc-abcc_qc.hdf5
 sub-01/ses-1mo/func/sub-01_ses-1mo_task-rest_acq-PA_run-001_desc-preproc_design.json

xcp_d/tests/data/test_pnc_cifti_outputs.txt

@@ -23,7 +23,6 @@ sub-1648798153.html
 sub-1648798153/ses-PNC1
 sub-1648798153/ses-PNC1/anat
 sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-MNI152NLin6Asym_desc-preproc_T1w.nii.gz
-sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-MNI152NLin6Asym_dseg.nii.gz
 sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-fsLR_den-32k_hemi-L_desc-hcp_inflated.surf.gii
 sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-fsLR_den-32k_hemi-L_desc-hcp_midthickness.surf.gii
 sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-fsLR_den-32k_hemi-L_desc-hcp_vinflated.surf.gii

xcp_d/tests/data/test_pnc_cifti_t2wonly_outputs.txt

@@ -19,7 +19,6 @@ sub-1648798153.html
 sub-1648798153/ses-PNC1
 sub-1648798153/ses-PNC1/anat
 sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-MNI152NLin6Asym_desc-preproc_T2w.nii.gz
-sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-MNI152NLin6Asym_dseg.nii.gz
 sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-fsLR_den-32k_hemi-L_desc-hcp_inflated.surf.gii
 sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-fsLR_den-32k_hemi-L_desc-hcp_midthickness.surf.gii
 sub-1648798153/ses-PNC1/anat/sub-1648798153_ses-PNC1_acq-refaced_space-fsLR_den-32k_hemi-L_desc-hcp_vinflated.surf.gii

xcp_d/tests/data/test_ukbiobank_outputs.txt

@@ -67,7 +67,6 @@ sub-0000001
 sub-0000001.html
 sub-0000001/ses-01
 sub-0000001/ses-01/anat
-sub-0000001/ses-01/anat/sub-0000001_ses-01_space-MNI152NLin6Asym_desc-aparcaseg_dseg.nii.gz
 sub-0000001/ses-01/anat/sub-0000001_ses-01_space-MNI152NLin6Asym_desc-preproc_T1w.nii.gz
 sub-0000001/ses-01/func
 sub-0000001/ses-01/func/sub-0000001_ses-01_task-rest_desc-filtered_motion.json

xcp_d/tests/test_workflows_anatomical.py

@@ -100,7 +100,6 @@ def test_postprocess_anat_wf(ds001419_data, tmp_path_factory):
 
     anat_to_template_xfm = ds001419_data["anat_to_template_xfm"]
     t1w = ds001419_data["t1w"]
-    anat_dseg = ds001419_data["anat_dseg"]
     t2w = os.path.join(tmpdir, "sub-01_desc-preproc_T2w.nii.gz")  # pretend t1w is t2w
     shutil.copyfile(t1w, t2w)
 
@@ -119,7 +118,6 @@ def test_postprocess_anat_wf(ds001419_data, tmp_path_factory):
 
         wf.inputs.inputnode.anat_to_template_xfm = anat_to_template_xfm
         wf.inputs.inputnode.t1w = t1w
-        wf.inputs.inputnode.anat_dseg = anat_dseg
         wf.inputs.inputnode.t2w = t2w
         wf.base_dir = tmpdir
         wf_res = wf.run()
@@ -132,6 +130,3 @@ def test_postprocess_anat_wf(ds001419_data, tmp_path_factory):
 
         out_t2w = wf_nodes["postprocess_anat_wf.ds_t2w_std"].get_output("out_file")
         assert os.path.isfile(out_t2w), os.listdir(out_anat_dir)
-
-        out_anat_dseg = wf_nodes["postprocess_anat_wf.ds_anat_dseg_std"].get_output("out_file")
-        assert os.path.isfile(out_anat_dseg), os.listdir(out_anat_dir)

xcp_d/utils/bids.py

@@ -173,8 +173,6 @@ def collect_data(
         # HCP/DCAN data have anats only in standard space
         queries["t1w"]["space"] = "MNI152NLin6Asym"
         queries["t2w"]["space"] = "MNI152NLin6Asym"
-        queries["anat_dseg"]["desc"] = "aparcaseg"
-        queries["anat_dseg"]["space"] = "MNI152NLin6Asym"
         queries["anat_brainmask"]["space"] = "MNI152NLin6Asym"
 
     queries["bold"]["extension"] = ".dtseries.nii" if (file_format == "cifti") else ".nii.gz"
@@ -299,14 +297,10 @@ def collect_data(
                     queries["t1w"]["space"] = ["T1w", None]
                     queries["template_to_anat_xfm"]["to"] = "T1w"
                     queries["anat_to_template_xfm"]["from"] = "T1w"
-                    # Nibabies may include space-T1w for some derivatives
-                    queries["anat_dseg"]["space"] = ["T1w", None]
                 else:
                     LOGGER.info("Performing T2w-only processing.")
                     queries["template_to_anat_xfm"]["to"] = "T2w"
                     queries["anat_to_template_xfm"]["from"] = "T2w"
-                    # Nibabies may include space-T2w for some derivatives
-                    queries["anat_dseg"]["space"] = ["T2w", None]
             else:
                 LOGGER.warning("T2w-space T1w found. Processing anatomical images in T2w space.")
         else:
@@ -317,8 +311,6 @@ def collect_data(
         LOGGER.warning("T2w found, but no T1w. Enabling T2w-only processing.")
         queries["template_to_anat_xfm"]["to"] = "T2w"
         queries["anat_to_template_xfm"]["from"] = "T2w"
-        # Nibabies may include space-T2w for some derivatives
-        queries["anat_dseg"]["space"] = ["T2w", None]
 
     # Search for the files.
     subj_data = {

xcp_d/workflows/anatomical/volume.py

@@ -63,8 +63,6 @@ def init_postprocess_anat_wf(
     t2w : :obj:`str` or None
         Path to the preprocessed T2w file.
         This file may be in standard space or native T1w space.
-    anat_dseg : :obj:`str`
-        Path to the T1w segmentation file.
     %(anat_to_template_xfm)s
         We need to use MNI152NLin6Asym for the template.
     template : :obj:`str`
@@ -87,7 +85,6 @@ def init_postprocess_anat_wf(
             fields=[
                 "t1w",
                 "t2w",
-                "anat_dseg",
                 "anat_to_template_xfm",
                 "template",
             ],
@@ -110,19 +107,6 @@ def init_postprocess_anat_wf(
     )
     inputnode.inputs.template = template_file
 
-    ds_anat_dseg_std = pe.Node(
-        DerivativesDataSink(
-            base_directory=output_dir,
-            space=target_space,
-            cohort=cohort,
-            extension=".nii.gz",
-        ),
-        name="ds_anat_dseg_std",
-        run_without_submitting=False,
-    )
-
-    workflow.connect([(inputnode, ds_anat_dseg_std, [("anat_dseg", "source_file")])])
-
     if t1w_available:
         ds_t1w_std = pe.Node(
             DerivativesDataSink(
@@ -156,45 +140,22 @@ def init_postprocess_anat_wf(
         ])  # fmt:skip
 
     if input_type in ("dcan", "hcp", "ukb"):
-        # Assume that the T1w, T1w segmentation, and T2w files are in standard space,
+        # Assume that the T1w and T2w files are in standard space,
         # but don't have the "space" entity, for the "dcan" and "hcp" derivatives.
         # This is a bug, and the converted filenames are inaccurate, so we have this
         # workaround in place.
-        workflow.connect([(inputnode, ds_anat_dseg_std, [("anat_dseg", "in_file")])])
-
         if t1w_available:
             workflow.connect([(inputnode, ds_t1w_std, [("t1w", "in_file")])])
 
         if t2w_available:
             workflow.connect([(inputnode, ds_t2w_std, [("t2w", "in_file")])])
 
     else:
-        out = (
-            ["T1w"] if t1w_available else [] + ["T2w"] if t2w_available else [] + ["segmentation"]
-        )
+        out = ["T1w"] if t1w_available else [] + ["T2w"] if t2w_available else []
         workflow.__desc__ = f"""\
 Native-space {list_to_str(out)} images were transformed to {target_space} space at 1 mm3
 resolution.
 """
-        warp_anat_dseg_to_template = pe.Node(
-            ApplyTransforms(
-                num_threads=2,
-                interpolation="GenericLabel",
-                input_image_type=3,
-                dimension=3,
-            ),
-            name="warp_anat_dseg_to_template",
-            mem_gb=2,
-            n_procs=omp_nthreads,
-        )
-        workflow.connect([
-            (inputnode, warp_anat_dseg_to_template, [
-                ("anat_dseg", "input_image"),
-                ("anat_to_template_xfm", "transforms"),
-                ("template", "reference_image"),
-            ]),
-            (warp_anat_dseg_to_template, ds_anat_dseg_std, [("output_image", "in_file")]),
-        ])  # fmt:skip
 
         if t1w_available:
             # Warp the native T1w-space T1w, T1w segmentation, and T2w files to standard space.

xcp_d/workflows/base.py

@@ -157,7 +157,6 @@ def init_single_subject_wf(subject_id: str):
                 "t1w",
                 "t2w",  # optional
                 "anat_brainmask",  # used to estimate head radius and for QC metrics
-                "anat_dseg",
                 "template_to_anat_xfm",  # not used by cifti workflow
                 "anat_to_template_xfm",
                 # mesh files
@@ -181,7 +180,6 @@ def init_single_subject_wf(subject_id: str):
     inputnode.inputs.t1w = subj_data["t1w"]
     inputnode.inputs.t2w = subj_data["t2w"]
     inputnode.inputs.anat_brainmask = subj_data["anat_brainmask"]
-    inputnode.inputs.anat_dseg = subj_data["anat_dseg"]
     inputnode.inputs.template_to_anat_xfm = subj_data["template_to_anat_xfm"]
     inputnode.inputs.anat_to_template_xfm = subj_data["anat_to_template_xfm"]
 
@@ -291,7 +289,6 @@ def init_single_subject_wf(subject_id: str):
         (inputnode, postprocess_anat_wf, [
             ("t1w", "inputnode.t1w"),
             ("t2w", "inputnode.t2w"),
-            ("anat_dseg", "inputnode.anat_dseg"),
             ("anat_to_template_xfm", "inputnode.anat_to_template_xfm"),
         ]),
     ])  # fmt:skip
@@ -467,7 +464,7 @@ def init_single_subject_wf(subject_id: str):
                 t2w_available=t2w_available,
                 n_runs=n_runs,
                 exact_scans=exact_scans,
-                name=f"{config.workflow.file_format}_postprocess_{run_counter}_wf",
+                name=f"postprocess_{run_counter}_wf",
             )
             run_counter += 1