junifer 0.0.4.dev821__tar.gz → 0.0.4.dev829__tar.gz

{junifer-0.0.4.dev821 → junifer-0.0.4.dev829}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.4.dev821
+Version: 0.0.4.dev829
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>

junifer-0.0.4.dev829/docs/changes/newsfragments/322.bugfix

@@ -0,0 +1 @@
+Force ``str`` dtype when parsing elements from file by `Synchon Mandal`_

junifer-0.0.4.dev829/docs/changes/newsfragments/325.change

@@ -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`_

{junifer-0.0.4.dev821 → junifer-0.0.4.dev829}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.4.dev821'
-__version_tuple__ = version_tuple = (0, 0, 4, 'dev821')
+__version__ = version = '0.0.4.dev829'
+__version_tuple__ = version_tuple = (0, 0, 4, 'dev829')

{junifer-0.0.4.dev821 → junifer-0.0.4.dev829}/junifer/api/cli.py

@@ -114,14 +114,13 @@ def _parse_elements_file(filepath: Path) -> List[Tuple[str, ...]]:
         filepath,
         header=None,  # no header  # type: ignore
         index_col=False,  # no index column
+        dtype=str,
         skipinitialspace=True,  # no leading space after delimiter
     )
     # Remove trailing whitespace in cell entries
-    csv_df_trimmed = csv_df.apply(
-        lambda x: x.str.strip() if x.dtype == "object" else x
-    )
+    csv_df_trimmed = csv_df.apply(lambda x: x.str.strip())
     # Convert to list of tuple of str
-    return list(map(tuple, csv_df_trimmed.to_numpy().astype(str)))
+    return list(map(tuple, csv_df_trimmed.to_numpy()))
 
 
 def _validate_verbose(

{junifer-0.0.4.dev821 → junifer-0.0.4.dev829}/junifer/api/tests/test_cli.py

@@ -156,6 +156,21 @@ def test_run_using_element_file(tmp_path: Path, elements: str) -> None:
             " sub-01 , ses-01 \n sub-02, ses-01 ",
             [("sub-01", "ses-01"), ("sub-02", "ses-01")],
         ),
+        ("001,01", [("001", "01")]),
+        (
+            "001,01\n002,02",
+            [("001", "01"), ("002", "02")],
+        ),
+        ("001, 01", [("001", "01")]),
+        (
+            "001, 01\n002, 02",
+            [("001", "01"), ("002", "02")],
+        ),
+        (" 001 , 01 ", [("001", "01")]),
+        (
+            " 001 , 01 \n 002, 02 ",
+            [("001", "01"), ("002", "02")],
+        ),
     ],
 )
 def test_multi_element_access(

{junifer-0.0.4.dev821 → junifer-0.0.4.dev829}/junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py

@@ -33,7 +33,7 @@ class JuselessDataladAOMICID1000VBM(PatternDataladDataGrabber):
         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",
             },

{junifer-0.0.4.dev821 → junifer-0.0.4.dev829}/junifer/configs/juseless/datagrabbers/camcan_vbm.py

@@ -36,7 +36,7 @@ class JuselessDataladCamCANVBM(PatternDataladDataGrabber):
         replacements = ["subject"]
         patterns = {
             "VBM_GM": {
-                "pattern": "sub-{subject}/mri/m0wp1sub-{subject}.nii.gz",
+                "pattern": "{subject}/mri/m0wp1{subject}.nii.gz",
                 "space": "IXI549Space",
             },
         }

{junifer-0.0.4.dev821 → junifer-0.0.4.dev829}/junifer/configs/juseless/datagrabbers/ixi_vbm.py

@@ -45,7 +45,7 @@ class JuselessDataladIXIVBM(PatternDataladDataGrabber):
         patterns = {
             "VBM_GM": {
                 "pattern": (
-                    "{site}/sub-{subject}/mri/m0wp1sub-{subject}.nii.gz"
+                    "{site}/{subject}/mri/m0wp1{subject}.nii.gz"
                 ),
                 "space": "IXI549Space",
             },

{junifer-0.0.4.dev821 → junifer-0.0.4.dev829}/junifer/configs/juseless/datagrabbers/ucla.py

@@ -72,42 +72,42 @@ class JuselessUCLA(PatternDataGrabber):
         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",

{junifer-0.0.4.dev821 → junifer-0.0.4.dev829}/junifer/configs/juseless/datagrabbers/ukb_vbm.py

@@ -34,7 +34,7 @@ class JuselessDataladUKBVBM(PatternDataladDataGrabber):
         replacements = ["subject", "session"]
         patterns = {
             "VBM_GM": {
-                "pattern": "m0wp1sub-{subject}_ses-{session}_T1w.nii.gz",
+                "pattern": "m0wp1{subject}_ses-{session}_T1w.nii.gz",
                 "space": "IXI549Space",
             },
         }

{junifer-0.0.4.dev821 → junifer-0.0.4.dev829}/junifer/data/tests/test_masks.py

@@ -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"],

{junifer-0.0.4.dev821 → junifer-0.0.4.dev829}/junifer/datagrabber/aomic/id1000.py

@@ -43,8 +43,8 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
         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",
@@ -52,16 +52,16 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
             },
             "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"
                 ),
@@ -69,8 +69,8 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
             },
             "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",
@@ -78,40 +78,40 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
             },
             "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"
                 ),
             },
         }
@@ -123,23 +123,23 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
                 {
                     "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",

{junifer-0.0.4.dev821 → junifer-0.0.4.dev829}/junifer/datagrabber/aomic/piop1.py

@@ -79,8 +79,8 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
         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",
@@ -88,24 +88,24 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
             },
             "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",
@@ -113,40 +113,40 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
             },
             "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"
                 ),
             },
         }
@@ -158,23 +158,23 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
                 {
                     "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",
@@ -242,7 +242,7 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
             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))

{junifer-0.0.4.dev821 → junifer-0.0.4.dev829}/junifer/datagrabber/aomic/piop2.py

@@ -76,8 +76,8 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
         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",
@@ -85,24 +85,24 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
             },
             "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",
@@ -110,40 +110,40 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
             },
             "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"
                 ),
             },
         }
@@ -155,23 +155,23 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
                 {
                     "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",
@@ -208,7 +208,7 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
             imposing constraints based on specified tasks.
 
         """
-        subjects = [f"{x:04d}" for x in range(1, 227)]
+        subjects = [f"sub-{x:04d}" for x in range(1, 227)]
         elems = []
         for subject, task in product(subjects, self.tasks):
             elems.append((subject, task))

{junifer-0.0.4.dev821 → junifer-0.0.4.dev829}/junifer/datagrabber/aomic/tests/test_id1000.py

@@ -34,7 +34,7 @@ def test_DataladAOMICID1000() -> None:
 
         assert (
             out["BOLD"]["path"].name
-            == f"sub-{test_element}_task-moviewatching_"
+            == f"{test_element}_task-moviewatching_"
             "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
         )
 
@@ -46,7 +46,7 @@ def test_DataladAOMICID1000() -> None:
 
         assert (
             out["BOLD_confounds"]["path"].name
-            == f"sub-{test_element}_task-moviewatching_"
+            == f"{test_element}_task-moviewatching_"
             "desc-confounds_regressors.tsv"
         )
 
@@ -61,7 +61,7 @@ def test_DataladAOMICID1000() -> None:
 
         assert (
             out["T1w"]["path"].name
-            == f"sub-{test_element}_space-MNI152NLin2009cAsym_"
+            == f"{test_element}_space-MNI152NLin2009cAsym_"
             "desc-preproc_T1w.nii.gz"
         )
 
@@ -76,7 +76,7 @@ def test_DataladAOMICID1000() -> None:
 
         assert (
             out["VBM_CSF"]["path"].name
-            == f"sub-{test_element}_space-MNI152NLin2009cAsym_label-"
+            == f"{test_element}_space-MNI152NLin2009cAsym_label-"
             "CSF_probseg.nii.gz"
         )
 
@@ -88,7 +88,7 @@ def test_DataladAOMICID1000() -> None:
 
         assert (
             out["VBM_GM"]["path"].name
-            == f"sub-{test_element}_space-MNI152NLin2009cAsym_label-"
+            == f"{test_element}_space-MNI152NLin2009cAsym_label-"
             "GM_probseg.nii.gz"
         )
 
@@ -100,7 +100,7 @@ def test_DataladAOMICID1000() -> None:
 
         assert (
             out["VBM_WM"]["path"].name
-            == f"sub-{test_element}_space-MNI152NLin2009cAsym_label-"
+            == f"{test_element}_space-MNI152NLin2009cAsym_label-"
             "WM_probseg.nii.gz"
         )
 
@@ -112,7 +112,7 @@ def test_DataladAOMICID1000() -> None:
 
         assert (
             out["DWI"]["path"].name
-            == f"sub-{test_element}_desc-preproc_dwi.nii.gz"
+            == f"{test_element}_desc-preproc_dwi.nii.gz"
         )
 
         assert out["DWI"]["path"].exists()