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Merge pull request #255 from mgxd/dep/bump-nipreps
ENH: Add morphometric outputs
2 parents 83056b0 + e674204 commit e151e67

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‎.circleci/bcp_anat_outputs.txt‎

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@@ -22,14 +22,20 @@ sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-fsnative_to-T1w_mode-image_xfm.t
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-MNIInfant+1_to-T1w_mode-image_xfm.h5
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-T1w_to-fsnative_mode-image_xfm.txt
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-T1w_to-MNIInfant+1_mode-image_xfm.h5
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_curv.shape.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_inflated.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_midthickness.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_pial.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_smoothwm.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_sulc.shape.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_thickness.shape.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_curv.shape.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_inflated.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_midthickness.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_pial.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_smoothwm.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_sulc.shape.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_thickness.shape.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_label-CSF_probseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_label-GM_probseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_label-WM_probseg.nii.gz

‎.circleci/bcp_full_outputs.txt‎

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@@ -22,14 +22,20 @@ sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-fsnative_to-T1w_mode-image_xfm.t
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-MNIInfant+1_to-T1w_mode-image_xfm.h5
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-T1w_to-fsnative_mode-image_xfm.txt
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-T1w_to-MNIInfant+1_mode-image_xfm.h5
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_curv.shape.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_inflated.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_midthickness.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_pial.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_smoothwm.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_sulc.shape.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_thickness.shape.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_curv.shape.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_inflated.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_midthickness.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_pial.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_smoothwm.surf.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_sulc.shape.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_thickness.shape.gii
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_label-CSF_probseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_label-GM_probseg.nii.gz
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sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_label-WM_probseg.nii.gz

‎.circleci/config.yml‎

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@@ -379,7 +379,6 @@ jobs:
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mkdir -p /tmp/${DATASET}/test
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CHECK_OUTPUTS_FILE="${DATASET}_full_outputs.txt"
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cd /tmp/${DATASET}/derivatives/nibabies && tree -I 'figures|log' -lifa --noreport | sed s+^\./++ | sed '1d' | sort > /tmp/${DATASET}/test/outputs.out
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cat /tmp/${DATASET}/test/outputs.out
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diff /tmp/src/nibabies/.circleci/${CHECK_OUTPUTS_FILE} /tmp/${DATASET}/test/outputs.out
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rm -rf /tmp/${DATASET}/test
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exit $?

‎.github/workflows/pytest.yml‎

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@@ -13,7 +13,7 @@ jobs:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: [3.7, 3.8, 3.9]
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python-version: ['3.8', '3.9', '3.10']
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steps:
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- name: Set up Python ${{ matrix.python-version }}

‎.readthedocs.yml‎

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@@ -1,7 +1,7 @@
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version: 2
22

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python:
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version: 3.7
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version: 3.8
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install:
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- requirements: docs/requirements.txt
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- method: pip

‎nibabies/cli/parser.py‎

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@@ -450,12 +450,6 @@ def _slice_time_ref(value, parser):
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default=True,
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help="do not remove median (within mask) from fieldmap",
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)
453-
g_fmap.add_argument(
454-
"--topup-max-vols",
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default=5,
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type=int,
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help="maximum number of volumes to use with TOPUP, per-series (EPI or BOLD)",
458-
)
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# SyN-unwarp options
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g_syn = parser.add_argument_group("Specific options for SyN distortion correction")

‎nibabies/workflows/anatomical/base.py‎

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@@ -141,6 +141,7 @@ def init_infant_anat_wf(
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"t1w2fsnative_xfm",
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"fsnative2t1w_xfm",
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"surfaces",
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"morphometrics",
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"anat_aseg",
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"anat_aparc",
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"template",
@@ -401,6 +402,7 @@ def init_infant_anat_wf(
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("outputnode.t1w2fsnative_xfm", "t1w2fsnative_xfm"),
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("outputnode.fsnative2t1w_xfm", "fsnative2t1w_xfm"),
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("outputnode.surfaces", "surfaces"),
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("outputnode.morphometrics", "morphometrics"),
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("outputnode.out_aparc", "anat_aparc"),
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("outputnode.out_aseg", "anat_aseg"),
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]),
@@ -414,6 +416,7 @@ def init_infant_anat_wf(
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("outputnode.t1w2fsnative_xfm", "inputnode.t1w2fsnative_xfm"),
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("outputnode.fsnative2t1w_xfm", "inputnode.fsnative2t1w_xfm"),
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("outputnode.surfaces", "inputnode.surfaces"),
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("outputnode.morphometrics", "inputnode.morphometrics"),
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]),
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])
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# fmt: on

‎nibabies/workflows/anatomical/outputs.py‎

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@@ -138,6 +138,8 @@ def init_anat_reports_wf(*, freesurfer, output_dir, sloppy, name="anat_reports_w
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"std_mask",
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"subject_id",
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"subjects_dir",
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"surfaces",
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"morphometrics",
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]
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inputnode = pe.Node(niu.IdentityInterface(fields=inputfields), name="inputnode")
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@@ -336,6 +338,7 @@ def init_anat_derivatives_wf(
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"t1w2fsnative_xfm",
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"fsnative2t1w_xfm",
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"surfaces",
341+
"morphometrics",
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"t1w_fs_aseg",
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"t1w_fs_aparc",
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]
@@ -636,6 +639,19 @@ def init_anat_derivatives_wf(
636639
name="ds_surfs",
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run_without_submitting=True,
638641
)
642+
# Morphometrics
643+
name_morphs = pe.MapNode(
644+
Path2BIDS(),
645+
iterfield="in_file",
646+
name="name_morphs",
647+
run_without_submitting=True,
648+
)
649+
ds_morphs = pe.MapNode(
650+
DerivativesDataSink(base_directory=output_dir, extension=".shape.gii"),
651+
iterfield=["in_file", "hemi", "suffix"],
652+
name="ds_morphs",
653+
run_without_submitting=True,
654+
)
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# Parcellations
640656
ds_t1w_fsaseg = pe.Node(
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DerivativesDataSink(base_directory=output_dir, desc="aseg", suffix="dseg", compress=True),
@@ -663,6 +679,11 @@ def init_anat_derivatives_wf(
663679
('source_files', 'source_file')]),
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(name_surfs, ds_surfs, [('hemi', 'hemi'),
665681
('suffix', 'suffix')]),
682+
(inputnode, name_morphs, [('morphometrics', 'in_file')]),
683+
(inputnode, ds_morphs, [('morphometrics', 'in_file'),
684+
('source_files', 'source_file')]),
685+
(name_morphs, ds_morphs, [('hemi', 'hemi'),
686+
('suffix', 'suffix')]),
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(inputnode, ds_t1w_fsaseg, [('t1w_fs_aseg', 'in_file'),
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('source_files', 'source_file')]),
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(inputnode, ds_t1w_fsparc, [('t1w_fs_aparc', 'in_file'),

‎nibabies/workflows/anatomical/surfaces.py‎

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@@ -40,6 +40,7 @@ def init_infant_surface_recon_wf(*, age_months, use_aseg=False, name="infant_sur
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"t1w2fsnative_xfm",
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"fsnative2t1w_xfm",
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"surfaces",
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"morphometrics",
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"out_aseg",
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"out_aparc",
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]
@@ -129,6 +130,7 @@ def init_infant_surface_recon_wf(*, age_months, use_aseg=False, name="infant_sur
129130
('out_reg_file', 'inputnode.fsnative2t1w_xfm')]),
130131
(gifti_surface_wf, outputnode, [
131132
('outputnode.surfaces', 'surfaces'),
133+
('outputnode.morphometrics', 'morphometrics'),
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]),
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])
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# fmt: on

‎nibabies/workflows/base.py‎

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@@ -548,9 +548,6 @@ def init_single_subject_wf(subject_id, session_id=None):
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fmap_wf_inputs = getattr(fmap_wf.inputs, f"in_{estimator.bids_id}")
549549
fmap_wf_inputs.in_data = [str(s.path) for s in estimator.sources]
550550
fmap_wf_inputs.metadata = [s.metadata for s in estimator.sources]
551-
552-
flatten = fmap_wf.get_node(f"wf_{estimator.bids_id}.flatten")
553-
flatten.inputs.max_trs = config.workflow.topup_max_vols
554551
else:
555552
raise NotImplementedError(
556553
"Sophisticated PEPOLAR schemes (e.g., using DWI+EPI) are unsupported."

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