junifer 0.0.4.dev821__py3-none-any.whl → 0.0.4.dev829__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (27) hide show
  1. junifer/_version.py +2 -2
  2. junifer/api/cli.py +3 -4
  3. junifer/api/tests/test_cli.py +15 -0
  4. junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py +1 -1
  5. junifer/configs/juseless/datagrabbers/camcan_vbm.py +1 -1
  6. junifer/configs/juseless/datagrabbers/ixi_vbm.py +1 -1
  7. junifer/configs/juseless/datagrabbers/ucla.py +6 -6
  8. junifer/configs/juseless/datagrabbers/ukb_vbm.py +1 -1
  9. junifer/data/tests/test_masks.py +2 -2
  10. junifer/datagrabber/aomic/id1000.py +24 -24
  11. junifer/datagrabber/aomic/piop1.py +25 -25
  12. junifer/datagrabber/aomic/piop2.py +25 -25
  13. junifer/datagrabber/aomic/tests/test_id1000.py +7 -7
  14. junifer/datagrabber/aomic/tests/test_piop1.py +7 -7
  15. junifer/datagrabber/aomic/tests/test_piop2.py +7 -7
  16. junifer/datagrabber/dmcc13_benchmark.py +45 -45
  17. junifer/datagrabber/tests/test_dmcc13_benchmark.py +33 -33
  18. junifer/preprocess/ants/tests/test_ants_apply_transforms_warper.py +2 -2
  19. junifer/preprocess/tests/test_bold_warper.py +6 -6
  20. junifer/preprocess/warping/tests/test_space_warper.py +6 -6
  21. {junifer-0.0.4.dev821.dist-info → junifer-0.0.4.dev829.dist-info}/METADATA +1 -1
  22. {junifer-0.0.4.dev821.dist-info → junifer-0.0.4.dev829.dist-info}/RECORD +27 -27
  23. {junifer-0.0.4.dev821.dist-info → junifer-0.0.4.dev829.dist-info}/AUTHORS.rst +0 -0
  24. {junifer-0.0.4.dev821.dist-info → junifer-0.0.4.dev829.dist-info}/LICENSE.md +0 -0
  25. {junifer-0.0.4.dev821.dist-info → junifer-0.0.4.dev829.dist-info}/WHEEL +0 -0
  26. {junifer-0.0.4.dev821.dist-info → junifer-0.0.4.dev829.dist-info}/entry_points.txt +0 -0
  27. {junifer-0.0.4.dev821.dist-info → junifer-0.0.4.dev829.dist-info}/top_level.txt +0 -0
junifer/_version.py CHANGED
@@ -12,5 +12,5 @@ __version__: str
12
12
  __version_tuple__: VERSION_TUPLE
13
13
  version_tuple: VERSION_TUPLE
14
14
 
15
- __version__ = version = '0.0.4.dev821'
16
- __version_tuple__ = version_tuple = (0, 0, 4, 'dev821')
15
+ __version__ = version = '0.0.4.dev829'
16
+ __version_tuple__ = version_tuple = (0, 0, 4, 'dev829')
junifer/api/cli.py CHANGED
@@ -114,14 +114,13 @@ def _parse_elements_file(filepath: Path) -> List[Tuple[str, ...]]:
114
114
  filepath,
115
115
  header=None, # no header # type: ignore
116
116
  index_col=False, # no index column
117
+ dtype=str,
117
118
  skipinitialspace=True, # no leading space after delimiter
118
119
  )
119
120
  # Remove trailing whitespace in cell entries
120
- csv_df_trimmed = csv_df.apply(
121
- lambda x: x.str.strip() if x.dtype == "object" else x
122
- )
121
+ csv_df_trimmed = csv_df.apply(lambda x: x.str.strip())
123
122
  # Convert to list of tuple of str
124
- return list(map(tuple, csv_df_trimmed.to_numpy().astype(str)))
123
+ return list(map(tuple, csv_df_trimmed.to_numpy()))
125
124
 
126
125
 
127
126
  def _validate_verbose(
junifer/api/tests/test_cli.py CHANGED
@@ -156,6 +156,21 @@ def test_run_using_element_file(tmp_path: Path, elements: str) -> None:
156
156
  " sub-01 , ses-01 \n sub-02, ses-01 ",
157
157
  [("sub-01", "ses-01"), ("sub-02", "ses-01")],
158
158
  ),
159
+ ("001,01", [("001", "01")]),
160
+ (
161
+ "001,01\n002,02",
162
+ [("001", "01"), ("002", "02")],
163
+ ),
164
+ ("001, 01", [("001", "01")]),
165
+ (
166
+ "001, 01\n002, 02",
167
+ [("001", "01"), ("002", "02")],
168
+ ),
169
+ (" 001 , 01 ", [("001", "01")]),
170
+ (
171
+ " 001 , 01 \n 002, 02 ",
172
+ [("001", "01"), ("002", "02")],
173
+ ),
159
174
  ],
160
175
  )
161
176
  def test_multi_element_access(
junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py CHANGED
@@ -33,7 +33,7 @@ class JuselessDataladAOMICID1000VBM(PatternDataladDataGrabber):
33
33
  patterns = {
34
34
  "VBM_GM": {
35
35
  "pattern": (
36
- "sub-{subject}/mri/mwp1sub-{subject}_run-2_T1w.nii.gz"
36
+ "{subject}/mri/mwp1{subject}_run-2_T1w.nii.gz"
37
37
  ),
38
38
  "space": "IXI549Space",
39
39
  },
junifer/configs/juseless/datagrabbers/camcan_vbm.py CHANGED
@@ -36,7 +36,7 @@ class JuselessDataladCamCANVBM(PatternDataladDataGrabber):
36
36
  replacements = ["subject"]
37
37
  patterns = {
38
38
  "VBM_GM": {
39
- "pattern": "sub-{subject}/mri/m0wp1sub-{subject}.nii.gz",
39
+ "pattern": "{subject}/mri/m0wp1{subject}.nii.gz",
40
40
  "space": "IXI549Space",
41
41
  },
42
42
  }
junifer/configs/juseless/datagrabbers/ixi_vbm.py CHANGED
@@ -45,7 +45,7 @@ class JuselessDataladIXIVBM(PatternDataladDataGrabber):
45
45
  patterns = {
46
46
  "VBM_GM": {
47
47
  "pattern": (
48
- "{site}/sub-{subject}/mri/m0wp1sub-{subject}.nii.gz"
48
+ "{site}/{subject}/mri/m0wp1{subject}.nii.gz"
49
49
  ),
50
50
  "space": "IXI549Space",
51
51
  },
junifer/configs/juseless/datagrabbers/ucla.py CHANGED
@@ -72,42 +72,42 @@ class JuselessUCLA(PatternDataGrabber):
72
72
  patterns = {
73
73
  "BOLD": {
74
74
  "pattern": (
75
- "sub-{subject}/func/sub-{subject}_task-{task}_bold_space-"
75
+ "{subject}/func/{subject}_task-{task}_bold_space-"
76
76
  "MNI152NLin2009cAsym_preproc.nii.gz"
77
77
  ),
78
78
  "space": "MNI152NLin2009cAsym",
79
79
  },
80
80
  "BOLD_confounds": {
81
81
  "pattern": (
82
- "sub-{subject}/func/sub-{subject}_"
82
+ "{subject}/func/{subject}_"
83
83
  "task-{task}_bold_confounds.tsv"
84
84
  ),
85
85
  "space": "fmriprep",
86
86
  },
87
87
  "T1w": {
88
88
  "pattern": (
89
- "sub-{subject}/anat/sub-{subject}_"
89
+ "{subject}/anat/{subject}_"
90
90
  "T1w_space-MNI152NLin2009cAsym_preproc.nii.gz"
91
91
  ),
92
92
  "space": "MNI152NLin2009cAsym",
93
93
  },
94
94
  "VBM_CSF": {
95
95
  "pattern": (
96
- "sub-{subject}/anat/sub-{subject}_T1w_space-"
96
+ "{subject}/anat/{subject}_T1w_space-"
97
97
  "MNI152NLin2009cAsym_class-CSF_probtissue.nii.gz"
98
98
  ),
99
99
  "space": "MNI152NLin2009cAsym",
100
100
  },
101
101
  "VBM_GM": {
102
102
  "pattern": (
103
- "sub-{subject}/anat/sub-{subject}_T1w_space-"
103
+ "{subject}/anat/{subject}_T1w_space-"
104
104
  "MNI152NLin2009cAsym_class-GM_probtissue.nii.gz"
105
105
  ),
106
106
  "space": "MNI152NLin2009cAsym",
107
107
  },
108
108
  "VBM_WM": {
109
109
  "pattern": (
110
- "sub-{subject}/anat/sub-{subject}_T1w_space"
110
+ "{subject}/anat/{subject}_T1w_space"
111
111
  "-MNI152NLin2009cAsym_class-WM_probtissue.nii.gz"
112
112
  ),
113
113
  "space": "MNI152NLin2009cAsym",
junifer/configs/juseless/datagrabbers/ukb_vbm.py CHANGED
@@ -34,7 +34,7 @@ class JuselessDataladUKBVBM(PatternDataladDataGrabber):
34
34
  replacements = ["subject", "session"]
35
35
  patterns = {
36
36
  "VBM_GM": {
37
- "pattern": "m0wp1sub-{subject}_ses-{session}_T1w.nii.gz",
37
+ "pattern": "m0wp1{subject}_ses-{session}_T1w.nii.gz",
38
38
  "space": "IXI549Space",
39
39
  },
40
40
  }
junifer/data/tests/test_masks.py CHANGED
@@ -96,14 +96,14 @@ def test_compute_brain_mask_for_native(mask_type: str) -> None:
96
96
  """
97
97
  with DMCC13Benchmark(
98
98
  types=["BOLD"],
99
- sessions=["wave1bas"],
99
+ sessions=["ses-wave1bas"],
100
100
  tasks=["Rest"],
101
101
  phase_encodings=["AP"],
102
102
  runs=["1"],
103
103
  native_t1w=True,
104
104
  ) as dg:
105
105
  element_data = DefaultDataReader().fit_transform(
106
- dg[("f1031ax", "wave1bas", "Rest", "AP", "1")]
106
+ dg[("sub-f1031ax", "ses-wave1bas", "Rest", "AP", "1")]
107
107
  )
108
108
  mask = compute_brain_mask(
109
109
  target_data=element_data["BOLD"],
junifer/datagrabber/aomic/id1000.py CHANGED
@@ -43,8 +43,8 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
43
43
  patterns = {
44
44
  "BOLD": {
45
45
  "pattern": (
46
- "derivatives/fmriprep/sub-{subject}/func/"
47
- "sub-{subject}_task-moviewatching_"
46
+ "derivatives/fmriprep/{subject}/func/"
47
+ "{subject}_task-moviewatching_"
48
48
  "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
49
49
  ),
50
50
  "space": "MNI152NLin2009cAsym",
@@ -52,16 +52,16 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
52
52
  },
53
53
  "BOLD_confounds": {
54
54
  "pattern": (
55
- "derivatives/fmriprep/sub-{subject}/func/"
56
- "sub-{subject}_task-moviewatching_"
55
+ "derivatives/fmriprep/{subject}/func/"
56
+ "{subject}_task-moviewatching_"
57
57
  "desc-confounds_regressors.tsv"
58
58
  ),
59
59
  "format": "fmriprep",
60
60
  },
61
61
  "BOLD_mask": {
62
62
  "pattern": (
63
- "derivatives/fmriprep/sub-{subject}/func/"
64
- "sub-{subject}_task-moviewatching_"
63
+ "derivatives/fmriprep/{subject}/func/"
64
+ "{subject}_task-moviewatching_"
65
65
  "space-MNI152NLin2009cAsym_"
66
66
  "desc-brain_mask.nii.gz"
67
67
  ),
@@ -69,8 +69,8 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
69
69
  },
70
70
  "T1w": {
71
71
  "pattern": (
72
- "derivatives/fmriprep/sub-{subject}/anat/"
73
- "sub-{subject}_space-MNI152NLin2009cAsym_"
72
+ "derivatives/fmriprep/{subject}/anat/"
73
+ "{subject}_space-MNI152NLin2009cAsym_"
74
74
  "desc-preproc_T1w.nii.gz"
75
75
  ),
76
76
  "space": "MNI152NLin2009cAsym",
@@ -78,40 +78,40 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
78
78
  },
79
79
  "T1w_mask": {
80
80
  "pattern": (
81
- "derivatives/fmriprep/sub-{subject}/anat/"
82
- "sub-{subject}_space-MNI152NLin2009cAsym_"
81
+ "derivatives/fmriprep/{subject}/anat/"
82
+ "{subject}_space-MNI152NLin2009cAsym_"
83
83
  "desc-brain_mask.nii.gz"
84
84
  ),
85
85
  "space": "MNI152NLin2009cAsym",
86
86
  },
87
87
  "VBM_CSF": {
88
88
  "pattern": (
89
- "derivatives/fmriprep/sub-{subject}/anat/"
90
- "sub-{subject}_space-MNI152NLin2009cAsym_label-"
89
+ "derivatives/fmriprep/{subject}/anat/"
90
+ "{subject}_space-MNI152NLin2009cAsym_label-"
91
91
  "CSF_probseg.nii.gz"
92
92
  ),
93
93
  "space": "MNI152NLin2009cAsym",
94
94
  },
95
95
  "VBM_GM": {
96
96
  "pattern": (
97
- "derivatives/fmriprep/sub-{subject}/anat/"
98
- "sub-{subject}_space-MNI152NLin2009cAsym_label-"
97
+ "derivatives/fmriprep/{subject}/anat/"
98
+ "{subject}_space-MNI152NLin2009cAsym_label-"
99
99
  "GM_probseg.nii.gz"
100
100
  ),
101
101
  "space": "MNI152NLin2009cAsym",
102
102
  },
103
103
  "VBM_WM": {
104
104
  "pattern": (
105
- "derivatives/fmriprep/sub-{subject}/anat/"
106
- "sub-{subject}_space-MNI152NLin2009cAsym_label-"
105
+ "derivatives/fmriprep/{subject}/anat/"
106
+ "{subject}_space-MNI152NLin2009cAsym_label-"
107
107
  "WM_probseg.nii.gz"
108
108
  ),
109
109
  "space": "MNI152NLin2009cAsym",
110
110
  },
111
111
  "DWI": {
112
112
  "pattern": (
113
- "derivatives/dwipreproc/sub-{subject}/dwi/"
114
- "sub-{subject}_desc-preproc_dwi.nii.gz"
113
+ "derivatives/dwipreproc/{subject}/dwi/"
114
+ "{subject}_desc-preproc_dwi.nii.gz"
115
115
  ),
116
116
  },
117
117
  }
@@ -123,23 +123,23 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
123
123
  {
124
124
  "T1w": {
125
125
  "pattern": (
126
- "derivatives/fmriprep/sub-{subject}/anat/"
127
- "sub-{subject}_desc-preproc_T1w.nii.gz"
126
+ "derivatives/fmriprep/{subject}/anat/"
127
+ "{subject}_desc-preproc_T1w.nii.gz"
128
128
  ),
129
129
  "space": "native",
130
130
  "mask_item": "T1w_mask",
131
131
  },
132
132
  "T1w_mask": {
133
133
  "pattern": (
134
- "derivatives/fmriprep/sub-{subject}/anat/"
135
- "sub-{subject}_desc-brain_mask.nii.gz"
134
+ "derivatives/fmriprep/{subject}/anat/"
135
+ "{subject}_desc-brain_mask.nii.gz"
136
136
  ),
137
137
  "space": "native",
138
138
  },
139
139
  "Warp": {
140
140
  "pattern": (
141
- "derivatives/fmriprep/sub-{subject}/anat/"
142
- "sub-{subject}_from-MNI152NLin2009cAsym_to-T1w_"
141
+ "derivatives/fmriprep/{subject}/anat/"
142
+ "{subject}_from-MNI152NLin2009cAsym_to-T1w_"
143
143
  "mode-image_xfm.h5"
144
144
  ),
145
145
  "src": "MNI152NLin2009cAsym",
junifer/datagrabber/aomic/piop1.py CHANGED
@@ -79,8 +79,8 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
79
79
  patterns = {
80
80
  "BOLD": {
81
81
  "pattern": (
82
- "derivatives/fmriprep/sub-{subject}/func/"
83
- "sub-{subject}_task-{task}_"
82
+ "derivatives/fmriprep/{subject}/func/"
83
+ "{subject}_task-{task}_"
84
84
  "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
85
85
  ),
86
86
  "space": "MNI152NLin2009cAsym",
@@ -88,24 +88,24 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
88
88
  },
89
89
  "BOLD_confounds": {
90
90
  "pattern": (
91
- "derivatives/fmriprep/sub-{subject}/func/"
92
- "sub-{subject}_task-{task}_"
91
+ "derivatives/fmriprep/{subject}/func/"
92
+ "{subject}_task-{task}_"
93
93
  "desc-confounds_regressors.tsv"
94
94
  ),
95
95
  "format": "fmriprep",
96
96
  },
97
97
  "BOLD_mask": {
98
98
  "pattern": (
99
- "derivatives/fmriprep/sub-{subject}/func/"
100
- "sub-{subject}_task-{task}_"
99
+ "derivatives/fmriprep/{subject}/func/"
100
+ "{subject}_task-{task}_"
101
101
  "space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
102
102
  ),
103
103
  "space": "MNI152NLin2009cAsym",
104
104
  },
105
105
  "T1w": {
106
106
  "pattern": (
107
- "derivatives/fmriprep/sub-{subject}/anat/"
108
- "sub-{subject}_space-MNI152NLin2009cAsym_"
107
+ "derivatives/fmriprep/{subject}/anat/"
108
+ "{subject}_space-MNI152NLin2009cAsym_"
109
109
  "desc-preproc_T1w.nii.gz"
110
110
  ),
111
111
  "space": "MNI152NLin2009cAsym",
@@ -113,40 +113,40 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
113
113
  },
114
114
  "T1w_mask": {
115
115
  "pattern": (
116
- "derivatives/fmriprep/sub-{subject}/anat/"
117
- "sub-{subject}_space-MNI152NLin2009cAsym_"
116
+ "derivatives/fmriprep/{subject}/anat/"
117
+ "{subject}_space-MNI152NLin2009cAsym_"
118
118
  "desc-brain_mask.nii.gz"
119
119
  ),
120
120
  "space": "MNI152NLin2009cAsym",
121
121
  },
122
122
  "VBM_CSF": {
123
123
  "pattern": (
124
- "derivatives/fmriprep/sub-{subject}/anat/"
125
- "sub-{subject}_space-MNI152NLin2009cAsym_label-"
124
+ "derivatives/fmriprep/{subject}/anat/"
125
+ "{subject}_space-MNI152NLin2009cAsym_label-"
126
126
  "CSF_probseg.nii.gz"
127
127
  ),
128
128
  "space": "MNI152NLin2009cAsym",
129
129
  },
130
130
  "VBM_GM": {
131
131
  "pattern": (
132
- "derivatives/fmriprep/sub-{subject}/anat/"
133
- "sub-{subject}_space-MNI152NLin2009cAsym_label-"
132
+ "derivatives/fmriprep/{subject}/anat/"
133
+ "{subject}_space-MNI152NLin2009cAsym_label-"
134
134
  "GM_probseg.nii.gz"
135
135
  ),
136
136
  "space": "MNI152NLin2009cAsym",
137
137
  },
138
138
  "VBM_WM": {
139
139
  "pattern": (
140
- "derivatives/fmriprep/sub-{subject}/anat/"
141
- "sub-{subject}_space-MNI152NLin2009cAsym_label-"
140
+ "derivatives/fmriprep/{subject}/anat/"
141
+ "{subject}_space-MNI152NLin2009cAsym_label-"
142
142
  "WM_probseg.nii.gz"
143
143
  ),
144
144
  "space": "MNI152NLin2009cAsym",
145
145
  },
146
146
  "DWI": {
147
147
  "pattern": (
148
- "derivatives/dwipreproc/sub-{subject}/dwi/"
149
- "sub-{subject}_desc-preproc_dwi.nii.gz"
148
+ "derivatives/dwipreproc/{subject}/dwi/"
149
+ "{subject}_desc-preproc_dwi.nii.gz"
150
150
  ),
151
151
  },
152
152
  }
@@ -158,23 +158,23 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
158
158
  {
159
159
  "T1w": {
160
160
  "pattern": (
161
- "derivatives/fmriprep/sub-{subject}/anat/"
162
- "sub-{subject}_desc-preproc_T1w.nii.gz"
161
+ "derivatives/fmriprep/{subject}/anat/"
162
+ "{subject}_desc-preproc_T1w.nii.gz"
163
163
  ),
164
164
  "space": "native",
165
165
  "mask_item": "T1w_mask",
166
166
  },
167
167
  "T1w_mask": {
168
168
  "pattern": (
169
- "derivatives/fmriprep/sub-{subject}/anat/"
170
- "sub-{subject}_desc-brain_mask.nii.gz"
169
+ "derivatives/fmriprep/{subject}/anat/"
170
+ "{subject}_desc-brain_mask.nii.gz"
171
171
  ),
172
172
  "space": "native",
173
173
  },
174
174
  "Warp": {
175
175
  "pattern": (
176
- "derivatives/fmriprep/sub-{subject}/anat/"
177
- "sub-{subject}_from-MNI152NLin2009cAsym_to-T1w_"
176
+ "derivatives/fmriprep/{subject}/anat/"
177
+ "{subject}_from-MNI152NLin2009cAsym_to-T1w_"
178
178
  "mode-image_xfm.h5"
179
179
  ),
180
180
  "src": "MNI152NLin2009cAsym",
@@ -242,7 +242,7 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
242
242
  The list of subjects in the dataset.
243
243
 
244
244
  """
245
- subjects = [f"{x:04d}" for x in range(1, 217)]
245
+ subjects = [f"sub-{x:04d}" for x in range(1, 217)]
246
246
  elems = []
247
247
  for subject, task in product(subjects, self.tasks):
248
248
  elems.append((subject, task))
junifer/datagrabber/aomic/piop2.py CHANGED
@@ -76,8 +76,8 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
76
76
  patterns = {
77
77
  "BOLD": {
78
78
  "pattern": (
79
- "derivatives/fmriprep/sub-{subject}/func/"
80
- "sub-{subject}_task-{task}_"
79
+ "derivatives/fmriprep/{subject}/func/"
80
+ "{subject}_task-{task}_"
81
81
  "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
82
82
  ),
83
83
  "space": "MNI152NLin2009cAsym",
@@ -85,24 +85,24 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
85
85
  },
86
86
  "BOLD_confounds": {
87
87
  "pattern": (
88
- "derivatives/fmriprep/sub-{subject}/func/"
89
- "sub-{subject}_task-{task}_"
88
+ "derivatives/fmriprep/{subject}/func/"
89
+ "{subject}_task-{task}_"
90
90
  "desc-confounds_regressors.tsv"
91
91
  ),
92
92
  "format": "fmriprep",
93
93
  },
94
94
  "BOLD_mask": {
95
95
  "pattern": (
96
- "derivatives/fmriprep/sub-{subject}/func/"
97
- "sub-{subject}_task-{task}_"
96
+ "derivatives/fmriprep/{subject}/func/"
97
+ "{subject}_task-{task}_"
98
98
  "space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
99
99
  ),
100
100
  "space": "MNI152NLin2009cAsym",
101
101
  },
102
102
  "T1w": {
103
103
  "pattern": (
104
- "derivatives/fmriprep/sub-{subject}/anat/"
105
- "sub-{subject}_space-MNI152NLin2009cAsym_"
104
+ "derivatives/fmriprep/{subject}/anat/"
105
+ "{subject}_space-MNI152NLin2009cAsym_"
106
106
  "desc-preproc_T1w.nii.gz"
107
107
  ),
108
108
  "space": "MNI152NLin2009cAsym",
@@ -110,40 +110,40 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
110
110
  },
111
111
  "T1w_mask": {
112
112
  "pattern": (
113
- "derivatives/fmriprep/sub-{subject}/anat/"
114
- "sub-{subject}_space-MNI152NLin2009cAsym_"
113
+ "derivatives/fmriprep/{subject}/anat/"
114
+ "{subject}_space-MNI152NLin2009cAsym_"
115
115
  "desc-brain_mask.nii.gz"
116
116
  ),
117
117
  "space": "MNI152NLin2009cAsym",
118
118
  },
119
119
  "VBM_CSF": {
120
120
  "pattern": (
121
- "derivatives/fmriprep/sub-{subject}/anat/"
122
- "sub-{subject}_space-MNI152NLin2009cAsym_label-"
121
+ "derivatives/fmriprep/{subject}/anat/"
122
+ "{subject}_space-MNI152NLin2009cAsym_label-"
123
123
  "CSF_probseg.nii.gz"
124
124
  ),
125
125
  "space": "MNI152NLin2009cAsym",
126
126
  },
127
127
  "VBM_GM": {
128
128
  "pattern": (
129
- "derivatives/fmriprep/sub-{subject}/anat/"
130
- "sub-{subject}_space-MNI152NLin2009cAsym_label-"
129
+ "derivatives/fmriprep/{subject}/anat/"
130
+ "{subject}_space-MNI152NLin2009cAsym_label-"
131
131
  "GM_probseg.nii.gz"
132
132
  ),
133
133
  "space": "MNI152NLin2009cAsym",
134
134
  },
135
135
  "VBM_WM": {
136
136
  "pattern": (
137
- "derivatives/fmriprep/sub-{subject}/anat/"
138
- "sub-{subject}_space-MNI152NLin2009cAsym_label-"
137
+ "derivatives/fmriprep/{subject}/anat/"
138
+ "{subject}_space-MNI152NLin2009cAsym_label-"
139
139
  "WM_probseg.nii.gz"
140
140
  ),
141
141
  "space": "MNI152NLin2009cAsym",
142
142
  },
143
143
  "DWI": {
144
144
  "pattern": (
145
- "derivatives/dwipreproc/sub-{subject}/dwi/"
146
- "sub-{subject}_desc-preproc_dwi.nii.gz"
145
+ "derivatives/dwipreproc/{subject}/dwi/"
146
+ "{subject}_desc-preproc_dwi.nii.gz"
147
147
  ),
148
148
  },
149
149
  }
@@ -155,23 +155,23 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
155
155
  {
156
156
  "T1w": {
157
157
  "pattern": (
158
- "derivatives/fmriprep/sub-{subject}/anat/"
159
- "sub-{subject}_desc-preproc_T1w.nii.gz"
158
+ "derivatives/fmriprep/{subject}/anat/"
159
+ "{subject}_desc-preproc_T1w.nii.gz"
160
160
  ),
161
161
  "space": "native",
162
162
  "mask_item": "T1w_mask",
163
163
  },
164
164
  "T1w_mask": {
165
165
  "pattern": (
166
- "derivatives/fmriprep/sub-{subject}/anat/"
167
- "sub-{subject}_desc-brain_mask.nii.gz"
166
+ "derivatives/fmriprep/{subject}/anat/"
167
+ "{subject}_desc-brain_mask.nii.gz"
168
168
  ),
169
169
  "space": "native",
170
170
  },
171
171
  "Warp": {
172
172
  "pattern": (
173
- "derivatives/fmriprep/sub-{subject}/anat/"
174
- "sub-{subject}_from-MNI152NLin2009cAsym_to-T1w_"
173
+ "derivatives/fmriprep/{subject}/anat/"
174
+ "{subject}_from-MNI152NLin2009cAsym_to-T1w_"
175
175
  "mode-image_xfm.h5"
176
176
  ),
177
177
  "src": "MNI152NLin2009cAsym",
@@ -208,7 +208,7 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
208
208
  imposing constraints based on specified tasks.
209
209
 
210
210
  """
211
- subjects = [f"{x:04d}" for x in range(1, 227)]
211
+ subjects = [f"sub-{x:04d}" for x in range(1, 227)]
212
212
  elems = []
213
213
  for subject, task in product(subjects, self.tasks):
214
214
  elems.append((subject, task))
junifer/datagrabber/aomic/tests/test_id1000.py CHANGED
@@ -34,7 +34,7 @@ def test_DataladAOMICID1000() -> None:
34
34
 
35
35
  assert (
36
36
  out["BOLD"]["path"].name
37
- == f"sub-{test_element}_task-moviewatching_"
37
+ == f"{test_element}_task-moviewatching_"
38
38
  "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
39
39
  )
40
40
 
@@ -46,7 +46,7 @@ def test_DataladAOMICID1000() -> None:
46
46
 
47
47
  assert (
48
48
  out["BOLD_confounds"]["path"].name
49
- == f"sub-{test_element}_task-moviewatching_"
49
+ == f"{test_element}_task-moviewatching_"
50
50
  "desc-confounds_regressors.tsv"
51
51
  )
52
52
 
@@ -61,7 +61,7 @@ def test_DataladAOMICID1000() -> None:
61
61
 
62
62
  assert (
63
63
  out["T1w"]["path"].name
64
- == f"sub-{test_element}_space-MNI152NLin2009cAsym_"
64
+ == f"{test_element}_space-MNI152NLin2009cAsym_"
65
65
  "desc-preproc_T1w.nii.gz"
66
66
  )
67
67
 
@@ -76,7 +76,7 @@ def test_DataladAOMICID1000() -> None:
76
76
 
77
77
  assert (
78
78
  out["VBM_CSF"]["path"].name
79
- == f"sub-{test_element}_space-MNI152NLin2009cAsym_label-"
79
+ == f"{test_element}_space-MNI152NLin2009cAsym_label-"
80
80
  "CSF_probseg.nii.gz"
81
81
  )
82
82
 
@@ -88,7 +88,7 @@ def test_DataladAOMICID1000() -> None:
88
88
 
89
89
  assert (
90
90
  out["VBM_GM"]["path"].name
91
- == f"sub-{test_element}_space-MNI152NLin2009cAsym_label-"
91
+ == f"{test_element}_space-MNI152NLin2009cAsym_label-"
92
92
  "GM_probseg.nii.gz"
93
93
  )
94
94
 
@@ -100,7 +100,7 @@ def test_DataladAOMICID1000() -> None:
100
100
 
101
101
  assert (
102
102
  out["VBM_WM"]["path"].name
103
- == f"sub-{test_element}_space-MNI152NLin2009cAsym_label-"
103
+ == f"{test_element}_space-MNI152NLin2009cAsym_label-"
104
104
  "WM_probseg.nii.gz"
105
105
  )
106
106
 
@@ -112,7 +112,7 @@ def test_DataladAOMICID1000() -> None:
112
112
 
113
113
  assert (
114
114
  out["DWI"]["path"].name
115
- == f"sub-{test_element}_desc-preproc_dwi.nii.gz"
115
+ == f"{test_element}_desc-preproc_dwi.nii.gz"
116
116
  )
117
117
 
118
118
  assert out["DWI"]["path"].exists()