junifer 0.0.4.dev782__py3-none-any.whl → 0.0.4.dev810__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 (30) hide show
  1. junifer/_version.py +2 -2
  2. junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py +6 -1
  3. junifer/configs/juseless/datagrabbers/camcan_vbm.py +6 -1
  4. junifer/configs/juseless/datagrabbers/ixi_vbm.py +6 -1
  5. junifer/configs/juseless/datagrabbers/ucla.py +42 -24
  6. junifer/configs/juseless/datagrabbers/ukb_vbm.py +6 -1
  7. junifer/datagrabber/aomic/id1000.py +98 -91
  8. junifer/datagrabber/aomic/piop1.py +97 -73
  9. junifer/datagrabber/aomic/piop2.py +97 -73
  10. junifer/datagrabber/base.py +6 -4
  11. junifer/datagrabber/datalad_base.py +0 -2
  12. junifer/datagrabber/dmcc13_benchmark.py +87 -50
  13. junifer/datagrabber/hcp1200/hcp1200.py +21 -19
  14. junifer/datagrabber/pattern.py +124 -25
  15. junifer/datagrabber/pattern_datalad.py +111 -13
  16. junifer/datagrabber/tests/test_base.py +0 -6
  17. junifer/datagrabber/tests/test_datagrabber_utils.py +204 -76
  18. junifer/datagrabber/tests/test_datalad_base.py +0 -6
  19. junifer/datagrabber/tests/test_multiple.py +43 -10
  20. junifer/datagrabber/tests/test_pattern.py +125 -178
  21. junifer/datagrabber/tests/test_pattern_datalad.py +44 -25
  22. junifer/datagrabber/utils.py +141 -21
  23. junifer/datareader/default.py +6 -7
  24. {junifer-0.0.4.dev782.dist-info → junifer-0.0.4.dev810.dist-info}/METADATA +1 -1
  25. {junifer-0.0.4.dev782.dist-info → junifer-0.0.4.dev810.dist-info}/RECORD +30 -30
  26. {junifer-0.0.4.dev782.dist-info → junifer-0.0.4.dev810.dist-info}/AUTHORS.rst +0 -0
  27. {junifer-0.0.4.dev782.dist-info → junifer-0.0.4.dev810.dist-info}/LICENSE.md +0 -0
  28. {junifer-0.0.4.dev782.dist-info → junifer-0.0.4.dev810.dist-info}/WHEEL +0 -0
  29. {junifer-0.0.4.dev782.dist-info → junifer-0.0.4.dev810.dist-info}/entry_points.txt +0 -0
  30. {junifer-0.0.4.dev782.dist-info → junifer-0.0.4.dev810.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.dev782'
16
- __version_tuple__ = version_tuple = (0, 0, 4, 'dev782')
15
+ __version__ = version = '0.0.4.dev810'
16
+ __version_tuple__ = version_tuple = (0, 0, 4, 'dev810')
junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py CHANGED
@@ -31,7 +31,12 @@ class JuselessDataladAOMICID1000VBM(PatternDataladDataGrabber):
31
31
  types = ["VBM_GM"]
32
32
  replacements = ["subject"]
33
33
  patterns = {
34
- "VBM_GM": "sub-{subject}/mri/mwp1sub-{subject}_run-2_T1w.nii.gz",
34
+ "VBM_GM": {
35
+ "pattern": (
36
+ "sub-{subject}/mri/mwp1sub-{subject}_run-2_T1w.nii.gz"
37
+ ),
38
+ "space": "IXI549Space",
39
+ },
35
40
  }
36
41
  super().__init__(
37
42
  types=types,
junifer/configs/juseless/datagrabbers/camcan_vbm.py CHANGED
@@ -34,7 +34,12 @@ class JuselessDataladCamCANVBM(PatternDataladDataGrabber):
34
34
  )
35
35
  types = ["VBM_GM"]
36
36
  replacements = ["subject"]
37
- patterns = {"VBM_GM": "sub-{subject}/mri/m0wp1sub-{subject}.nii.gz"}
37
+ patterns = {
38
+ "VBM_GM": {
39
+ "pattern": "sub-{subject}/mri/m0wp1sub-{subject}.nii.gz",
40
+ "space": "IXI549Space",
41
+ },
42
+ }
38
43
  super().__init__(
39
44
  types=types,
40
45
  datadir=datadir,
junifer/configs/juseless/datagrabbers/ixi_vbm.py CHANGED
@@ -43,7 +43,12 @@ class JuselessDataladIXIVBM(PatternDataladDataGrabber):
43
43
  types = ["VBM_GM"]
44
44
  replacements = ["site", "subject"]
45
45
  patterns = {
46
- "VBM_GM": "{site}/sub-{subject}/mri/m0wp1sub-{subject}.nii.gz"
46
+ "VBM_GM": {
47
+ "pattern": (
48
+ "{site}/sub-{subject}/mri/m0wp1sub-{subject}.nii.gz"
49
+ ),
50
+ "space": "IXI549Space",
51
+ },
47
52
  }
48
53
 
49
54
  # validate and/or transform 'site' input
junifer/configs/juseless/datagrabbers/ucla.py CHANGED
@@ -70,30 +70,48 @@ class JuselessUCLA(PatternDataGrabber):
70
70
  self.tasks = tasks
71
71
  # The patterns
72
72
  patterns = {
73
- "BOLD": (
74
- "sub-{subject}/func/sub-{subject}_task-{task}_bold_space-"
75
- "MNI152NLin2009cAsym_preproc.nii.gz"
76
- ),
77
- "BOLD_confounds": (
78
- "sub-{subject}/func/sub-{subject}_"
79
- "task-{task}_bold_confounds.tsv"
80
- ),
81
- "T1w": (
82
- "sub-{subject}/anat/sub-{subject}_"
83
- "T1w_space-MNI152NLin2009cAsym_preproc.nii.gz"
84
- ),
85
- "probseg_CSF": (
86
- "sub-{subject}/anat/sub-{subject}_T1w_space-"
87
- "MNI152NLin2009cAsym_class-CSF_probtissue.nii.gz"
88
- ),
89
- "probseg_GM": (
90
- "sub-{subject}/anat/sub-{subject}_T1w_space-"
91
- "MNI152NLin2009cAsym_class-GM_probtissue.nii.gz"
92
- ),
93
- "probseg_WM": (
94
- "sub-{subject}/anat/sub-{subject}_T1w_space"
95
- "-MNI152NLin2009cAsym_class-WM_probtissue.nii.gz"
96
- ),
73
+ "BOLD": {
74
+ "pattern": (
75
+ "sub-{subject}/func/sub-{subject}_task-{task}_bold_space-"
76
+ "MNI152NLin2009cAsym_preproc.nii.gz"
77
+ ),
78
+ "space": "MNI152NLin2009cAsym",
79
+ },
80
+ "BOLD_confounds": {
81
+ "pattern": (
82
+ "sub-{subject}/func/sub-{subject}_"
83
+ "task-{task}_bold_confounds.tsv"
84
+ ),
85
+ "space": "fmriprep",
86
+ },
87
+ "T1w": {
88
+ "pattern": (
89
+ "sub-{subject}/anat/sub-{subject}_"
90
+ "T1w_space-MNI152NLin2009cAsym_preproc.nii.gz"
91
+ ),
92
+ "space": "MNI152NLin2009cAsym",
93
+ },
94
+ "probseg_CSF": {
95
+ "pattern": (
96
+ "sub-{subject}/anat/sub-{subject}_T1w_space-"
97
+ "MNI152NLin2009cAsym_class-CSF_probtissue.nii.gz"
98
+ ),
99
+ "space": "MNI152NLin2009cAsym",
100
+ },
101
+ "probseg_GM": {
102
+ "pattern": (
103
+ "sub-{subject}/anat/sub-{subject}_T1w_space-"
104
+ "MNI152NLin2009cAsym_class-GM_probtissue.nii.gz"
105
+ ),
106
+ "space": "MNI152NLin2009cAsym",
107
+ },
108
+ "probseg_WM": {
109
+ "pattern": (
110
+ "sub-{subject}/anat/sub-{subject}_T1w_space"
111
+ "-MNI152NLin2009cAsym_class-WM_probtissue.nii.gz"
112
+ ),
113
+ "space": "MNI152NLin2009cAsym",
114
+ },
97
115
  }
98
116
  # Set default types
99
117
  if types is None:
junifer/configs/juseless/datagrabbers/ukb_vbm.py CHANGED
@@ -32,7 +32,12 @@ class JuselessDataladUKBVBM(PatternDataladDataGrabber):
32
32
  rootdir = "m0wp1"
33
33
  types = ["VBM_GM"]
34
34
  replacements = ["subject", "session"]
35
- patterns = {"VBM_GM": "m0wp1sub-{subject}_ses-{session}_T1w.nii.gz"}
35
+ patterns = {
36
+ "VBM_GM": {
37
+ "pattern": "m0wp1sub-{subject}_ses-{session}_T1w.nii.gz",
38
+ "space": "IXI549Space",
39
+ },
40
+ }
36
41
  super().__init__(
37
42
  types=types,
38
43
  datadir=datadir,
junifer/datagrabber/aomic/id1000.py CHANGED
@@ -8,7 +8,7 @@
8
8
  # License: AGPL
9
9
 
10
10
  from pathlib import Path
11
- from typing import Dict, List, Union
11
+ from typing import List, Union
12
12
 
13
13
  from ...api.decorators import register_datagrabber
14
14
  from ..pattern_datalad import PatternDataladDataGrabber
@@ -41,51 +41,79 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
41
41
  ) -> None:
42
42
  # The patterns
43
43
  patterns = {
44
- "BOLD": (
45
- "derivatives/fmriprep/sub-{subject}/func/"
46
- "sub-{subject}_task-moviewatching_"
47
- "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
48
- ),
49
- "BOLD_confounds": (
50
- "derivatives/fmriprep/sub-{subject}/func/"
51
- "sub-{subject}_task-moviewatching_"
52
- "desc-confounds_regressors.tsv"
53
- ),
54
- "BOLD_mask": (
55
- "derivatives/fmriprep/sub-{subject}/func/"
56
- "sub-{subject}_task-moviewatching_"
57
- "space-MNI152NLin2009cAsym_"
58
- "desc-brain_mask.nii.gz"
59
- ),
60
- "T1w": (
61
- "derivatives/fmriprep/sub-{subject}/anat/"
62
- "sub-{subject}_space-MNI152NLin2009cAsym_"
63
- "desc-preproc_T1w.nii.gz"
64
- ),
65
- "T1w_mask": (
66
- "derivatives/fmriprep/sub-{subject}/anat/"
67
- "sub-{subject}_space-MNI152NLin2009cAsym_"
68
- "desc-brain_mask.nii.gz"
69
- ),
70
- "probseg_CSF": (
71
- "derivatives/fmriprep/sub-{subject}/anat/"
72
- "sub-{subject}_space-MNI152NLin2009cAsym_label-"
73
- "CSF_probseg.nii.gz"
74
- ),
75
- "probseg_GM": (
76
- "derivatives/fmriprep/sub-{subject}/anat/"
77
- "sub-{subject}_space-MNI152NLin2009cAsym_label-"
78
- "GM_probseg.nii.gz"
79
- ),
80
- "probseg_WM": (
81
- "derivatives/fmriprep/sub-{subject}/anat/"
82
- "sub-{subject}_space-MNI152NLin2009cAsym_label-"
83
- "WM_probseg.nii.gz"
84
- ),
85
- "DWI": (
86
- "derivatives/dwipreproc/sub-{subject}/dwi/"
87
- "sub-{subject}_desc-preproc_dwi.nii.gz"
88
- ),
44
+ "BOLD": {
45
+ "pattern": (
46
+ "derivatives/fmriprep/sub-{subject}/func/"
47
+ "sub-{subject}_task-moviewatching_"
48
+ "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
49
+ ),
50
+ "space": "MNI152NLin2009cAsym",
51
+ "mask_item": "BOLD_mask",
52
+ },
53
+ "BOLD_confounds": {
54
+ "pattern": (
55
+ "derivatives/fmriprep/sub-{subject}/func/"
56
+ "sub-{subject}_task-moviewatching_"
57
+ "desc-confounds_regressors.tsv"
58
+ ),
59
+ "format": "fmriprep",
60
+ },
61
+ "BOLD_mask": {
62
+ "pattern": (
63
+ "derivatives/fmriprep/sub-{subject}/func/"
64
+ "sub-{subject}_task-moviewatching_"
65
+ "space-MNI152NLin2009cAsym_"
66
+ "desc-brain_mask.nii.gz"
67
+ ),
68
+ "space": "MNI152NLin2009cAsym",
69
+ },
70
+ "T1w": {
71
+ "pattern": (
72
+ "derivatives/fmriprep/sub-{subject}/anat/"
73
+ "sub-{subject}_space-MNI152NLin2009cAsym_"
74
+ "desc-preproc_T1w.nii.gz"
75
+ ),
76
+ "space": "MNI152NLin2009cAsym",
77
+ "mask_item": "T1w_mask",
78
+ },
79
+ "T1w_mask": {
80
+ "pattern": (
81
+ "derivatives/fmriprep/sub-{subject}/anat/"
82
+ "sub-{subject}_space-MNI152NLin2009cAsym_"
83
+ "desc-brain_mask.nii.gz"
84
+ ),
85
+ "space": "MNI152NLin2009cAsym",
86
+ },
87
+ "probseg_CSF": {
88
+ "pattern": (
89
+ "derivatives/fmriprep/sub-{subject}/anat/"
90
+ "sub-{subject}_space-MNI152NLin2009cAsym_label-"
91
+ "CSF_probseg.nii.gz"
92
+ ),
93
+ "space": "MNI152NLin2009cAsym",
94
+ },
95
+ "probseg_GM": {
96
+ "pattern": (
97
+ "derivatives/fmriprep/sub-{subject}/anat/"
98
+ "sub-{subject}_space-MNI152NLin2009cAsym_label-"
99
+ "GM_probseg.nii.gz"
100
+ ),
101
+ "space": "MNI152NLin2009cAsym",
102
+ },
103
+ "probseg_WM": {
104
+ "pattern": (
105
+ "derivatives/fmriprep/sub-{subject}/anat/"
106
+ "sub-{subject}_space-MNI152NLin2009cAsym_label-"
107
+ "WM_probseg.nii.gz"
108
+ ),
109
+ "space": "MNI152NLin2009cAsym",
110
+ },
111
+ "DWI": {
112
+ "pattern": (
113
+ "derivatives/dwipreproc/sub-{subject}/dwi/"
114
+ "sub-{subject}_desc-preproc_dwi.nii.gz"
115
+ ),
116
+ },
89
117
  }
90
118
  # Use native T1w assets
91
119
  self.native_t1w = False
@@ -93,19 +121,30 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
93
121
  self.native_t1w = True
94
122
  patterns.update(
95
123
  {
96
- "T1w": (
97
- "derivatives/fmriprep/sub-{subject}/anat/"
98
- "sub-{subject}_desc-preproc_T1w.nii.gz"
99
- ),
100
- "T1w_mask": (
101
- "derivatives/fmriprep/sub-{subject}/anat/"
102
- "sub-{subject}_desc-brain_mask.nii.gz"
103
- ),
104
- "Warp": (
105
- "derivatives/fmriprep/sub-{subject}/anat/"
106
- "sub-{subject}_from-MNI152NLin2009cAsym_to-T1w_"
107
- "mode-image_xfm.h5"
108
- ),
124
+ "T1w": {
125
+ "pattern": (
126
+ "derivatives/fmriprep/sub-{subject}/anat/"
127
+ "sub-{subject}_desc-preproc_T1w.nii.gz"
128
+ ),
129
+ "space": "native",
130
+ "mask_item": "T1w_mask",
131
+ },
132
+ "T1w_mask": {
133
+ "pattern": (
134
+ "derivatives/fmriprep/sub-{subject}/anat/"
135
+ "sub-{subject}_desc-brain_mask.nii.gz"
136
+ ),
137
+ "space": "native",
138
+ },
139
+ "Warp": {
140
+ "pattern": (
141
+ "derivatives/fmriprep/sub-{subject}/anat/"
142
+ "sub-{subject}_from-MNI152NLin2009cAsym_to-T1w_"
143
+ "mode-image_xfm.h5"
144
+ ),
145
+ "src": "MNI152NLin2009cAsym",
146
+ "dst": "native",
147
+ },
109
148
  }
110
149
  )
111
150
  # Set default types
@@ -126,35 +165,3 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
126
165
  replacements=replacements,
127
166
  confounds_format="fmriprep",
128
167
  )
129
-
130
- def get_item(self, subject: str) -> Dict:
131
- """Index one element in the dataset.
132
-
133
- Parameters
134
- ----------
135
- subject : str
136
- The subject ID.
137
-
138
- Returns
139
- -------
140
- out : dict
141
- Dictionary of paths for each type of data required for the
142
- specified element.
143
-
144
- """
145
- out = super().get_item(subject=subject)
146
- if out.get("BOLD"):
147
- out["BOLD"]["mask_item"] = "BOLD_mask"
148
- # Add space information
149
- out["BOLD"].update({"space": "MNI152NLin2009cAsym"})
150
- if out.get("T1w"):
151
- out["T1w"]["mask_item"] = "T1w_mask"
152
- # Add space information
153
- if self.native_t1w:
154
- out["T1w"].update({"space": "native"})
155
- else:
156
- out["T1w"].update({"space": "MNI152NLin2009cAsym"})
157
- if out.get("Warp"):
158
- # Add source space information
159
- out["Warp"].update({"src": "MNI152NLin2009cAsym"})
160
- return out
junifer/datagrabber/aomic/piop1.py CHANGED
@@ -77,50 +77,78 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
77
77
  self.tasks = tasks
78
78
  # The patterns
79
79
  patterns = {
80
- "BOLD": (
81
- "derivatives/fmriprep/sub-{subject}/func/"
82
- "sub-{subject}_task-{task}_"
83
- "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
84
- ),
85
- "BOLD_confounds": (
86
- "derivatives/fmriprep/sub-{subject}/func/"
87
- "sub-{subject}_task-{task}_"
88
- "desc-confounds_regressors.tsv"
89
- ),
90
- "BOLD_mask": (
91
- "derivatives/fmriprep/sub-{subject}/func/"
92
- "sub-{subject}_task-{task}_"
93
- "space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
94
- ),
95
- "T1w": (
96
- "derivatives/fmriprep/sub-{subject}/anat/"
97
- "sub-{subject}_space-MNI152NLin2009cAsym_"
98
- "desc-preproc_T1w.nii.gz"
99
- ),
100
- "T1w_mask": (
101
- "derivatives/fmriprep/sub-{subject}/anat/"
102
- "sub-{subject}_space-MNI152NLin2009cAsym_"
103
- "desc-brain_mask.nii.gz"
104
- ),
105
- "probseg_CSF": (
106
- "derivatives/fmriprep/sub-{subject}/anat/"
107
- "sub-{subject}_space-MNI152NLin2009cAsym_label-"
108
- "CSF_probseg.nii.gz"
109
- ),
110
- "probseg_GM": (
111
- "derivatives/fmriprep/sub-{subject}/anat/"
112
- "sub-{subject}_space-MNI152NLin2009cAsym_label-"
113
- "GM_probseg.nii.gz"
114
- ),
115
- "probseg_WM": (
116
- "derivatives/fmriprep/sub-{subject}/anat/"
117
- "sub-{subject}_space-MNI152NLin2009cAsym_label-"
118
- "WM_probseg.nii.gz"
119
- ),
120
- "DWI": (
121
- "derivatives/dwipreproc/sub-{subject}/dwi/"
122
- "sub-{subject}_desc-preproc_dwi.nii.gz"
123
- ),
80
+ "BOLD": {
81
+ "pattern": (
82
+ "derivatives/fmriprep/sub-{subject}/func/"
83
+ "sub-{subject}_task-{task}_"
84
+ "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
85
+ ),
86
+ "space": "MNI152NLin2009cAsym",
87
+ "mask_item": "BOLD_mask",
88
+ },
89
+ "BOLD_confounds": {
90
+ "pattern": (
91
+ "derivatives/fmriprep/sub-{subject}/func/"
92
+ "sub-{subject}_task-{task}_"
93
+ "desc-confounds_regressors.tsv"
94
+ ),
95
+ "format": "fmriprep",
96
+ },
97
+ "BOLD_mask": {
98
+ "pattern": (
99
+ "derivatives/fmriprep/sub-{subject}/func/"
100
+ "sub-{subject}_task-{task}_"
101
+ "space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
102
+ ),
103
+ "space": "MNI152NLin2009cAsym",
104
+ },
105
+ "T1w": {
106
+ "pattern": (
107
+ "derivatives/fmriprep/sub-{subject}/anat/"
108
+ "sub-{subject}_space-MNI152NLin2009cAsym_"
109
+ "desc-preproc_T1w.nii.gz"
110
+ ),
111
+ "space": "MNI152NLin2009cAsym",
112
+ "mask_item": "T1w_mask",
113
+ },
114
+ "T1w_mask": {
115
+ "pattern": (
116
+ "derivatives/fmriprep/sub-{subject}/anat/"
117
+ "sub-{subject}_space-MNI152NLin2009cAsym_"
118
+ "desc-brain_mask.nii.gz"
119
+ ),
120
+ "space": "MNI152NLin2009cAsym",
121
+ },
122
+ "probseg_CSF": {
123
+ "pattern": (
124
+ "derivatives/fmriprep/sub-{subject}/anat/"
125
+ "sub-{subject}_space-MNI152NLin2009cAsym_label-"
126
+ "CSF_probseg.nii.gz"
127
+ ),
128
+ "space": "MNI152NLin2009cAsym",
129
+ },
130
+ "probseg_GM": {
131
+ "pattern": (
132
+ "derivatives/fmriprep/sub-{subject}/anat/"
133
+ "sub-{subject}_space-MNI152NLin2009cAsym_label-"
134
+ "GM_probseg.nii.gz"
135
+ ),
136
+ "space": "MNI152NLin2009cAsym",
137
+ },
138
+ "probseg_WM": {
139
+ "pattern": (
140
+ "derivatives/fmriprep/sub-{subject}/anat/"
141
+ "sub-{subject}_space-MNI152NLin2009cAsym_label-"
142
+ "WM_probseg.nii.gz"
143
+ ),
144
+ "space": "MNI152NLin2009cAsym",
145
+ },
146
+ "DWI": {
147
+ "pattern": (
148
+ "derivatives/dwipreproc/sub-{subject}/dwi/"
149
+ "sub-{subject}_desc-preproc_dwi.nii.gz"
150
+ ),
151
+ },
124
152
  }
125
153
  # Use native T1w assets
126
154
  self.native_t1w = False
@@ -128,19 +156,30 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
128
156
  self.native_t1w = True
129
157
  patterns.update(
130
158
  {
131
- "T1w": (
132
- "derivatives/fmriprep/sub-{subject}/anat/"
133
- "sub-{subject}_desc-preproc_T1w.nii.gz"
134
- ),
135
- "T1w_mask": (
136
- "derivatives/fmriprep/sub-{subject}/anat/"
137
- "sub-{subject}_desc-brain_mask.nii.gz"
138
- ),
139
- "Warp": (
140
- "derivatives/fmriprep/sub-{subject}/anat/"
141
- "sub-{subject}_from-MNI152NLin2009cAsym_to-T1w_"
142
- "mode-image_xfm.h5"
143
- ),
159
+ "T1w": {
160
+ "pattern": (
161
+ "derivatives/fmriprep/sub-{subject}/anat/"
162
+ "sub-{subject}_desc-preproc_T1w.nii.gz"
163
+ ),
164
+ "space": "native",
165
+ "mask_item": "T1w_mask",
166
+ },
167
+ "T1w_mask": {
168
+ "pattern": (
169
+ "derivatives/fmriprep/sub-{subject}/anat/"
170
+ "sub-{subject}_desc-brain_mask.nii.gz"
171
+ ),
172
+ "space": "native",
173
+ },
174
+ "Warp": {
175
+ "pattern": (
176
+ "derivatives/fmriprep/sub-{subject}/anat/"
177
+ "sub-{subject}_from-MNI152NLin2009cAsym_to-T1w_"
178
+ "mode-image_xfm.h5"
179
+ ),
180
+ "src": "MNI152NLin2009cAsym",
181
+ "dst": "native",
182
+ },
144
183
  }
145
184
  )
146
185
  # Set default types
@@ -192,22 +231,7 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
192
231
  acq = task_acqs[task]
193
232
  new_task = f"{task}_acq-{acq}"
194
233
 
195
- out = super().get_item(subject=subject, task=new_task)
196
- if out.get("BOLD"):
197
- out["BOLD"]["mask_item"] = "BOLD_mask"
198
- # Add space information
199
- out["BOLD"].update({"space": "MNI152NLin2009cAsym"})
200
- if out.get("T1w"):
201
- out["T1w"]["mask_item"] = "T1w_mask"
202
- # Add space information
203
- if self.native_t1w:
204
- out["T1w"].update({"space": "native"})
205
- else:
206
- out["T1w"].update({"space": "MNI152NLin2009cAsym"})
207
- if out.get("Warp"):
208
- # Add source space information
209
- out["Warp"].update({"src": "MNI152NLin2009cAsym"})
210
- return out
234
+ return super().get_item(subject=subject, task=new_task)
211
235
 
212
236
  def get_elements(self) -> List:
213
237
  """Implement fetching list of subjects in the dataset.