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Merge pull request #325 from juaml/fix/bids
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Follow the datasets BIDS convention for participants/sessions
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@synchon
synchon authored Apr 5, 2024
2 parents 526014d + 6a7bc3d commit d868722
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Showing 18 changed files with 200 additions and 199 deletions.
1 change: 1 addition & 0 deletions docs/changes/newsfragments/325.change
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@@ -0,0 +1 @@
Change the subject and session patterns for :class:`.DataladAOMICID1000`, :class:`.DataladAOMICPIOP1`, :class:`.DataladAOMICPIOP2` and :class:`.DMCC13Benchmark` so that they are consistent with their own ``"participants.tsv"`` file by `Fede Raimondo`_
2 changes: 1 addition & 1 deletion junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py
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Expand Up @@ -33,7 +33,7 @@ def __init__(self, datadir: Union[str, Path, None] = None) -> None:
patterns = {
"VBM_GM": {
"pattern": (
"sub-{subject}/mri/mwp1sub-{subject}_run-2_T1w.nii.gz"
"{subject}/mri/mwp1{subject}_run-2_T1w.nii.gz"
),
"space": "IXI549Space",
},
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2 changes: 1 addition & 1 deletion junifer/configs/juseless/datagrabbers/camcan_vbm.py
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Expand Up @@ -36,7 +36,7 @@ def __init__(self, datadir: Union[str, Path, None] = None) -> None:
replacements = ["subject"]
patterns = {
"VBM_GM": {
"pattern": "sub-{subject}/mri/m0wp1sub-{subject}.nii.gz",
"pattern": "{subject}/mri/m0wp1{subject}.nii.gz",
"space": "IXI549Space",
},
}
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2 changes: 1 addition & 1 deletion junifer/configs/juseless/datagrabbers/ixi_vbm.py
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Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@ def __init__(
patterns = {
"VBM_GM": {
"pattern": (
"{site}/sub-{subject}/mri/m0wp1sub-{subject}.nii.gz"
"{site}/{subject}/mri/m0wp1{subject}.nii.gz"
),
"space": "IXI549Space",
},
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12 changes: 6 additions & 6 deletions junifer/configs/juseless/datagrabbers/ucla.py
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Expand Up @@ -72,42 +72,42 @@ def __init__(
patterns = {
"BOLD": {
"pattern": (
"sub-{subject}/func/sub-{subject}_task-{task}_bold_space-"
"{subject}/func/{subject}_task-{task}_bold_space-"
"MNI152NLin2009cAsym_preproc.nii.gz"
),
"space": "MNI152NLin2009cAsym",
},
"BOLD_confounds": {
"pattern": (
"sub-{subject}/func/sub-{subject}_"
"{subject}/func/{subject}_"
"task-{task}_bold_confounds.tsv"
),
"space": "fmriprep",
},
"T1w": {
"pattern": (
"sub-{subject}/anat/sub-{subject}_"
"{subject}/anat/{subject}_"
"T1w_space-MNI152NLin2009cAsym_preproc.nii.gz"
),
"space": "MNI152NLin2009cAsym",
},
"VBM_CSF": {
"pattern": (
"sub-{subject}/anat/sub-{subject}_T1w_space-"
"{subject}/anat/{subject}_T1w_space-"
"MNI152NLin2009cAsym_class-CSF_probtissue.nii.gz"
),
"space": "MNI152NLin2009cAsym",
},
"VBM_GM": {
"pattern": (
"sub-{subject}/anat/sub-{subject}_T1w_space-"
"{subject}/anat/{subject}_T1w_space-"
"MNI152NLin2009cAsym_class-GM_probtissue.nii.gz"
),
"space": "MNI152NLin2009cAsym",
},
"VBM_WM": {
"pattern": (
"sub-{subject}/anat/sub-{subject}_T1w_space"
"{subject}/anat/{subject}_T1w_space"
"-MNI152NLin2009cAsym_class-WM_probtissue.nii.gz"
),
"space": "MNI152NLin2009cAsym",
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2 changes: 1 addition & 1 deletion junifer/configs/juseless/datagrabbers/ukb_vbm.py
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Expand Up @@ -34,7 +34,7 @@ def __init__(self, datadir: Union[str, Path, None] = None) -> None:
replacements = ["subject", "session"]
patterns = {
"VBM_GM": {
"pattern": "m0wp1sub-{subject}_ses-{session}_T1w.nii.gz",
"pattern": "m0wp1{subject}_ses-{session}_T1w.nii.gz",
"space": "IXI549Space",
},
}
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4 changes: 2 additions & 2 deletions junifer/data/tests/test_masks.py
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Expand Up @@ -96,14 +96,14 @@ def test_compute_brain_mask_for_native(mask_type: str) -> None:
"""
with DMCC13Benchmark(
types=["BOLD"],
sessions=["wave1bas"],
sessions=["ses-wave1bas"],
tasks=["Rest"],
phase_encodings=["AP"],
runs=["1"],
native_t1w=True,
) as dg:
element_data = DefaultDataReader().fit_transform(
dg[("f1031ax", "wave1bas", "Rest", "AP", "1")]
dg[("sub-f1031ax", "ses-wave1bas", "Rest", "AP", "1")]
)
mask = compute_brain_mask(
target_data=element_data["BOLD"],
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48 changes: 24 additions & 24 deletions junifer/datagrabber/aomic/id1000.py
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Expand Up @@ -43,75 +43,75 @@ def __init__(
patterns = {
"BOLD": {
"pattern": (
"derivatives/fmriprep/sub-{subject}/func/"
"sub-{subject}_task-moviewatching_"
"derivatives/fmriprep/{subject}/func/"
"{subject}_task-moviewatching_"
"space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
),
"space": "MNI152NLin2009cAsym",
"mask_item": "BOLD_mask",
},
"BOLD_confounds": {
"pattern": (
"derivatives/fmriprep/sub-{subject}/func/"
"sub-{subject}_task-moviewatching_"
"derivatives/fmriprep/{subject}/func/"
"{subject}_task-moviewatching_"
"desc-confounds_regressors.tsv"
),
"format": "fmriprep",
},
"BOLD_mask": {
"pattern": (
"derivatives/fmriprep/sub-{subject}/func/"
"sub-{subject}_task-moviewatching_"
"derivatives/fmriprep/{subject}/func/"
"{subject}_task-moviewatching_"
"space-MNI152NLin2009cAsym_"
"desc-brain_mask.nii.gz"
),
"space": "MNI152NLin2009cAsym",
},
"T1w": {
"pattern": (
"derivatives/fmriprep/sub-{subject}/anat/"
"sub-{subject}_space-MNI152NLin2009cAsym_"
"derivatives/fmriprep/{subject}/anat/"
"{subject}_space-MNI152NLin2009cAsym_"
"desc-preproc_T1w.nii.gz"
),
"space": "MNI152NLin2009cAsym",
"mask_item": "T1w_mask",
},
"T1w_mask": {
"pattern": (
"derivatives/fmriprep/sub-{subject}/anat/"
"sub-{subject}_space-MNI152NLin2009cAsym_"
"derivatives/fmriprep/{subject}/anat/"
"{subject}_space-MNI152NLin2009cAsym_"
"desc-brain_mask.nii.gz"
),
"space": "MNI152NLin2009cAsym",
},
"VBM_CSF": {
"pattern": (
"derivatives/fmriprep/sub-{subject}/anat/"
"sub-{subject}_space-MNI152NLin2009cAsym_label-"
"derivatives/fmriprep/{subject}/anat/"
"{subject}_space-MNI152NLin2009cAsym_label-"
"CSF_probseg.nii.gz"
),
"space": "MNI152NLin2009cAsym",
},
"VBM_GM": {
"pattern": (
"derivatives/fmriprep/sub-{subject}/anat/"
"sub-{subject}_space-MNI152NLin2009cAsym_label-"
"derivatives/fmriprep/{subject}/anat/"
"{subject}_space-MNI152NLin2009cAsym_label-"
"GM_probseg.nii.gz"
),
"space": "MNI152NLin2009cAsym",
},
"VBM_WM": {
"pattern": (
"derivatives/fmriprep/sub-{subject}/anat/"
"sub-{subject}_space-MNI152NLin2009cAsym_label-"
"derivatives/fmriprep/{subject}/anat/"
"{subject}_space-MNI152NLin2009cAsym_label-"
"WM_probseg.nii.gz"
),
"space": "MNI152NLin2009cAsym",
},
"DWI": {
"pattern": (
"derivatives/dwipreproc/sub-{subject}/dwi/"
"sub-{subject}_desc-preproc_dwi.nii.gz"
"derivatives/dwipreproc/{subject}/dwi/"
"{subject}_desc-preproc_dwi.nii.gz"
),
},
}
Expand All @@ -123,23 +123,23 @@ def __init__(
{
"T1w": {
"pattern": (
"derivatives/fmriprep/sub-{subject}/anat/"
"sub-{subject}_desc-preproc_T1w.nii.gz"
"derivatives/fmriprep/{subject}/anat/"
"{subject}_desc-preproc_T1w.nii.gz"
),
"space": "native",
"mask_item": "T1w_mask",
},
"T1w_mask": {
"pattern": (
"derivatives/fmriprep/sub-{subject}/anat/"
"sub-{subject}_desc-brain_mask.nii.gz"
"derivatives/fmriprep/{subject}/anat/"
"{subject}_desc-brain_mask.nii.gz"
),
"space": "native",
},
"Warp": {
"pattern": (
"derivatives/fmriprep/sub-{subject}/anat/"
"sub-{subject}_from-MNI152NLin2009cAsym_to-T1w_"
"derivatives/fmriprep/{subject}/anat/"
"{subject}_from-MNI152NLin2009cAsym_to-T1w_"
"mode-image_xfm.h5"
),
"src": "MNI152NLin2009cAsym",
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50 changes: 25 additions & 25 deletions junifer/datagrabber/aomic/piop1.py
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Original file line number Diff line number Diff line change
Expand Up @@ -79,74 +79,74 @@ def __init__(
patterns = {
"BOLD": {
"pattern": (
"derivatives/fmriprep/sub-{subject}/func/"
"sub-{subject}_task-{task}_"
"derivatives/fmriprep/{subject}/func/"
"{subject}_task-{task}_"
"space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
),
"space": "MNI152NLin2009cAsym",
"mask_item": "BOLD_mask",
},
"BOLD_confounds": {
"pattern": (
"derivatives/fmriprep/sub-{subject}/func/"
"sub-{subject}_task-{task}_"
"derivatives/fmriprep/{subject}/func/"
"{subject}_task-{task}_"
"desc-confounds_regressors.tsv"
),
"format": "fmriprep",
},
"BOLD_mask": {
"pattern": (
"derivatives/fmriprep/sub-{subject}/func/"
"sub-{subject}_task-{task}_"
"derivatives/fmriprep/{subject}/func/"
"{subject}_task-{task}_"
"space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
),
"space": "MNI152NLin2009cAsym",
},
"T1w": {
"pattern": (
"derivatives/fmriprep/sub-{subject}/anat/"
"sub-{subject}_space-MNI152NLin2009cAsym_"
"derivatives/fmriprep/{subject}/anat/"
"{subject}_space-MNI152NLin2009cAsym_"
"desc-preproc_T1w.nii.gz"
),
"space": "MNI152NLin2009cAsym",
"mask_item": "T1w_mask",
},
"T1w_mask": {
"pattern": (
"derivatives/fmriprep/sub-{subject}/anat/"
"sub-{subject}_space-MNI152NLin2009cAsym_"
"derivatives/fmriprep/{subject}/anat/"
"{subject}_space-MNI152NLin2009cAsym_"
"desc-brain_mask.nii.gz"
),
"space": "MNI152NLin2009cAsym",
},
"VBM_CSF": {
"pattern": (
"derivatives/fmriprep/sub-{subject}/anat/"
"sub-{subject}_space-MNI152NLin2009cAsym_label-"
"derivatives/fmriprep/{subject}/anat/"
"{subject}_space-MNI152NLin2009cAsym_label-"
"CSF_probseg.nii.gz"
),
"space": "MNI152NLin2009cAsym",
},
"VBM_GM": {
"pattern": (
"derivatives/fmriprep/sub-{subject}/anat/"
"sub-{subject}_space-MNI152NLin2009cAsym_label-"
"derivatives/fmriprep/{subject}/anat/"
"{subject}_space-MNI152NLin2009cAsym_label-"
"GM_probseg.nii.gz"
),
"space": "MNI152NLin2009cAsym",
},
"VBM_WM": {
"pattern": (
"derivatives/fmriprep/sub-{subject}/anat/"
"sub-{subject}_space-MNI152NLin2009cAsym_label-"
"derivatives/fmriprep/{subject}/anat/"
"{subject}_space-MNI152NLin2009cAsym_label-"
"WM_probseg.nii.gz"
),
"space": "MNI152NLin2009cAsym",
},
"DWI": {
"pattern": (
"derivatives/dwipreproc/sub-{subject}/dwi/"
"sub-{subject}_desc-preproc_dwi.nii.gz"
"derivatives/dwipreproc/{subject}/dwi/"
"{subject}_desc-preproc_dwi.nii.gz"
),
},
}
Expand All @@ -158,23 +158,23 @@ def __init__(
{
"T1w": {
"pattern": (
"derivatives/fmriprep/sub-{subject}/anat/"
"sub-{subject}_desc-preproc_T1w.nii.gz"
"derivatives/fmriprep/{subject}/anat/"
"{subject}_desc-preproc_T1w.nii.gz"
),
"space": "native",
"mask_item": "T1w_mask",
},
"T1w_mask": {
"pattern": (
"derivatives/fmriprep/sub-{subject}/anat/"
"sub-{subject}_desc-brain_mask.nii.gz"
"derivatives/fmriprep/{subject}/anat/"
"{subject}_desc-brain_mask.nii.gz"
),
"space": "native",
},
"Warp": {
"pattern": (
"derivatives/fmriprep/sub-{subject}/anat/"
"sub-{subject}_from-MNI152NLin2009cAsym_to-T1w_"
"derivatives/fmriprep/{subject}/anat/"
"{subject}_from-MNI152NLin2009cAsym_to-T1w_"
"mode-image_xfm.h5"
),
"src": "MNI152NLin2009cAsym",
Expand Down Expand Up @@ -242,7 +242,7 @@ def get_elements(self) -> List:
The list of subjects in the dataset.
"""
subjects = [f"{x:04d}" for x in range(1, 217)]
subjects = [f"sub-{x:04d}" for x in range(1, 217)]
elems = []
for subject, task in product(subjects, self.tasks):
elems.append((subject, task))
Expand Down
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