junifer 0.0.3.dev188__py3-none-any.whl → 0.0.4__py3-none-any.whl

junifer/api/tests/test_parser.py

@@ -53,7 +53,7 @@ def test_parse_yaml_success_with_module_autoload(tmp_path: Path) -> None:
     assert "foo" in contents
     assert contents["foo"] == "bar"
     assert "with" in contents
-    assert contents["with"] == "numpy"
+    assert contents["with"] == ["numpy"]
     assert "numpy" in sys.modules
     assert "junifer.configs.wrong_config" not in sys.modules
 

junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py

@@ -31,7 +31,12 @@ class JuselessDataladAOMICID1000VBM(PatternDataladDataGrabber):
         types = ["VBM_GM"]
         replacements = ["subject"]
         patterns = {
-            "VBM_GM": "sub-{subject}/mri/mwp1sub-{subject}_run-2_T1w.nii.gz",
+            "VBM_GM": {
+                "pattern": (
+                    "{subject}/mri/mwp1{subject}_run-2_T1w.nii.gz"
+                ),
+                "space": "IXI549Space",
+            },
         }
         super().__init__(
             types=types,

junifer/configs/juseless/datagrabbers/camcan_vbm.py

@@ -34,7 +34,12 @@ class JuselessDataladCamCANVBM(PatternDataladDataGrabber):
         )
         types = ["VBM_GM"]
         replacements = ["subject"]
-        patterns = {"VBM_GM": "sub-{subject}/mri/m0wp1sub-{subject}.nii.gz"}
+        patterns = {
+            "VBM_GM": {
+                "pattern": "{subject}/mri/m0wp1{subject}.nii.gz",
+                "space": "IXI549Space",
+            },
+        }
         super().__init__(
             types=types,
             datadir=datadir,

junifer/configs/juseless/datagrabbers/ixi_vbm.py

@@ -43,7 +43,12 @@ class JuselessDataladIXIVBM(PatternDataladDataGrabber):
         types = ["VBM_GM"]
         replacements = ["site", "subject"]
         patterns = {
-            "VBM_GM": "{site}/sub-{subject}/mri/m0wp1sub-{subject}.nii.gz"
+            "VBM_GM": {
+                "pattern": (
+                    "{site}/{subject}/mri/m0wp1{subject}.nii.gz"
+                ),
+                "space": "IXI549Space",
+            },
         }
 
         # validate and/or transform 'site' input

junifer/configs/juseless/datagrabbers/tests/test_ucla.py

@@ -29,9 +29,9 @@ def test_JuselessUCLA() -> None:
             "BOLD",
             "BOLD_confounds",
             "T1w",
-            "probseg_CSF",
-            "probseg_GM",
-            "probseg_WM",
+            "VBM_CSF",
+            "VBM_GM",
+            "VBM_WM",
         ]
 
         for t in types:
@@ -45,12 +45,12 @@ def test_JuselessUCLA() -> None:
         "BOLD",
         "BOLD_confounds",
         "T1w",
-        "probseg_CSF",
-        "probseg_GM",
-        "probseg_WM",
+        "VBM_CSF",
+        "VBM_GM",
+        "VBM_WM",
         ["BOLD", "BOLD_confounds"],
-        ["T1w", "probseg_CSF"],
-        ["probseg_GM", "probseg_WM"],
+        ["T1w", "VBM_CSF"],
+        ["VBM_GM", "VBM_WM"],
         ["BOLD", "T1w"],
     ],
 )

junifer/configs/juseless/datagrabbers/ucla.py

@@ -23,8 +23,8 @@ class JuselessUCLA(PatternDataGrabber):
     datadir : str or Path, optional
         The directory where the dataset is stored.
         (default "/data/project/psychosis_thalamus/data/fmriprep").
-    types: {"BOLD", "BOLD_confounds", "T1w", "probseg_CSF", "probseg_GM", \
-           "probseg_WM"} or a list of the options, optional
+    types: {"BOLD", "BOLD_confounds", "T1w", "VBM_CSF", "VBM_GM", \
+           "VBM_WM"} or a list of the options, optional
         UCLA data types. If None, all available data types are selected.
         (default None).
     tasks : {"rest", "bart", "bht", "pamenc", "pamret", \
@@ -70,30 +70,48 @@ class JuselessUCLA(PatternDataGrabber):
         self.tasks = tasks
         # The patterns
         patterns = {
-            "BOLD": (
-                "sub-{subject}/func/sub-{subject}_task-{task}_bold_space-"
-                "MNI152NLin2009cAsym_preproc.nii.gz"
-            ),
-            "BOLD_confounds": (
-                "sub-{subject}/func/sub-{subject}_"
-                "task-{task}_bold_confounds.tsv"
-            ),
-            "T1w": (
-                "sub-{subject}/anat/sub-{subject}_"
-                "T1w_space-MNI152NLin2009cAsym_preproc.nii.gz"
-            ),
-            "probseg_CSF": (
-                "sub-{subject}/anat/sub-{subject}_T1w_space-"
-                "MNI152NLin2009cAsym_class-CSF_probtissue.nii.gz"
-            ),
-            "probseg_GM": (
-                "sub-{subject}/anat/sub-{subject}_T1w_space-"
-                "MNI152NLin2009cAsym_class-GM_probtissue.nii.gz"
-            ),
-            "probseg_WM": (
-                "sub-{subject}/anat/sub-{subject}_T1w_space"
-                "-MNI152NLin2009cAsym_class-WM_probtissue.nii.gz"
-            ),
+            "BOLD": {
+                "pattern": (
+                    "{subject}/func/{subject}_task-{task}_bold_space-"
+                    "MNI152NLin2009cAsym_preproc.nii.gz"
+                ),
+                "space": "MNI152NLin2009cAsym",
+            },
+            "BOLD_confounds": {
+                "pattern": (
+                    "{subject}/func/{subject}_"
+                    "task-{task}_bold_confounds.tsv"
+                ),
+                "space": "fmriprep",
+            },
+            "T1w": {
+                "pattern": (
+                    "{subject}/anat/{subject}_"
+                    "T1w_space-MNI152NLin2009cAsym_preproc.nii.gz"
+                ),
+                "space": "MNI152NLin2009cAsym",
+            },
+            "VBM_CSF": {
+                "pattern": (
+                    "{subject}/anat/{subject}_T1w_space-"
+                    "MNI152NLin2009cAsym_class-CSF_probtissue.nii.gz"
+                ),
+                "space": "MNI152NLin2009cAsym",
+            },
+            "VBM_GM": {
+                "pattern": (
+                    "{subject}/anat/{subject}_T1w_space-"
+                    "MNI152NLin2009cAsym_class-GM_probtissue.nii.gz"
+                ),
+                "space": "MNI152NLin2009cAsym",
+            },
+            "VBM_WM": {
+                "pattern": (
+                    "{subject}/anat/{subject}_T1w_space"
+                    "-MNI152NLin2009cAsym_class-WM_probtissue.nii.gz"
+                ),
+                "space": "MNI152NLin2009cAsym",
+            },
         }
         # Set default types
         if types is None:

junifer/configs/juseless/datagrabbers/ukb_vbm.py

@@ -32,7 +32,12 @@ class JuselessDataladUKBVBM(PatternDataladDataGrabber):
         rootdir = "m0wp1"
         types = ["VBM_GM"]
         replacements = ["subject", "session"]
-        patterns = {"VBM_GM": "m0wp1sub-{subject}_ses-{session}_T1w.nii.gz"}
+        patterns = {
+            "VBM_GM": {
+                "pattern": "m0wp1{subject}_ses-{session}_T1w.nii.gz",
+                "space": "IXI549Space",
+            },
+        }
         super().__init__(
             types=types,
             datadir=datadir,

junifer/data/VOIs/meta/AutobiographicalMemory_VOIs.txt

@@ -0,0 +1,23 @@
+-2	-53	18	PCu-PCC_LR
+-25	-26	-14	HC-PHC-AMG_L
+-47	-61	26	TPJ_L
+-3	47	-1	Medial-prefrontal-cortex_rACC(bilateral)_L
+-56	-8	-14	STS_MTG_inferior-temporal-sulcus_L
+-47	25	-5	Ventrolateral-prefrontal-cortex_temporal-pole_L
+23	-31	-12	HC-PHC_R
+-3	12	57	Middle-frontal-gyrus_LR
+49	-59	27	TPJ_R
+-45	3	45	Posterior-lateral-prefrontal-cortex_L
+-40	47	14	Frontal-pole(lateral)_L
+23	-13	-15	HC-PHC_R
+49	-5	-13	Temporal-pole_STS_MTG_R
+-37	14	-32	Temporal-pole_L
+-37	-81	30	Occ_L
+-46	24	21	Dorsolateral-prefrontal-cortex_L
+50	27	-5	Ventrolateral-prefrontal-cortex_R
+-11	55	17	Frontal_pole(medial)_L
+3	-9	5	Thalamus_R
+-5	33	22	rACC_L
+-6	-37	33	PCC_L
+-28	9	51	Superior-frontal-sulcus_L
+28	1	-19	AMG_R

junifer/data/VOIs/meta/Power2013_MNI_VOIs.tsv

@@ -0,0 +1,264 @@
+22	-65	48	1
+25	-58	60	2
+-35	20	0	3
+12	36	20	4
+40	18	40	5
+54	-28	34	6
+36	22	3	7
+59	-17	29	8
+-45	0	9	9
+46	-59	4	10
+-32	-1	54	11
+32	14	56	12
+-42	-60	-9	13
+-34	3	4	14
+37	1	-4	15
+29	-5	54	16
+11	-39	50	17
+37	-65	40	18
+-34	-38	-16	19
+-52	-63	5	20
+-10	11	67	21
+-44	2	46	22
+-3	26	44	23
+49	8	-1	24
+-33	-46	47	25
+-27	-71	37	26
+55	-45	37	27
+7	8	51	28
+36	10	1	29
+-39	51	17	30
+10	-62	61	31
+-16	-5	71	32
+43	49	-2	33
+37	32	-2	34
+10	-2	45	35
+47	-30	49	36
+36	-9	14	37
+-3	2	53	38
+-51	8	-2	39
+-1	15	44	40
+31	-14	2	41
+19	-8	64	42
+-10	-2	42	43
+65	-33	20	44
+-30	-27	12	45
+6	-72	24	46
+-7	-52	61	47
+-49	-42	1	48
+-49	25	-1	49
+-5	18	34	50
+-23	11	64	51
+31	33	26	52
+-0	30	27	53
+-53	-22	23	54
+-42	-55	45	55
+-50	-34	26	56
+48	22	10	57
+31	56	14	58
+44	-8	57	59
+49	35	-12	60
+-56	-50	10	61
+2	-24	30	62
+29	-39	59	63
+-42	-74	0	64
+-34	55	4	65
+13	-1	70	66
+42	-0	47	67
+-3	42	16	68
+5	23	37	69
+51	-29	-4	70
+0	-15	47	71
+52	-33	8	72
+34	16	-8	73
+-7	-71	42	74
+-29	-43	61	75
+33	-53	44	76
+-55	-40	14	77
+-17	-59	64	78
+56	-5	13	79
+46	-47	-17	80
+-11	26	25	81
+22	-42	69	82
+-13	-40	1	83
+43	-23	20	84
+-53	-49	43	85
+-47	11	23	86
+54	-43	22	87
+53	33	1	88
+10	22	27	89
+-55	-9	12	90
+-58	-30	-4	91
+-42	45	-2	92
+56	-46	11	93
+-45	-32	47	94
+11	-66	42	95
+-28	-79	19	96
+-47	-76	-10	97
+-2	38	36	98
+-54	-23	43	99
+-28	52	21	100
+47	-50	29	101
+-2	-35	31	102
+50	-20	42	103
+-42	38	21	104
+26	50	27	105
+58	-53	-14	106
+47	10	33	107
+32	-26	13	108
+-46	31	-13	109
+10	-46	73	110
+27	-37	-13	111
+43	-72	28	112
+52	-2	-16	113
+-2	-37	44	114
+38	43	15	115
+-60	-25	14	116
+-41	6	33	117
+-2	-13	12	118
+42	-66	-8	119
+9	-4	6	120
+29	1	4	121
+15	5	7	122
+-42	25	30	123
+-26	-40	-8	124
+65	-31	-9	125
+44	-53	47	126
+-18	-76	-24	127
+-35	20	51	128
+-28	-58	48	129
+-49	-26	5	130
+-53	-10	24	131
+-47	-51	-21	132
+58	-16	7	133
+49	-42	45	134
+40	-72	14	135
+-32	-55	-25	136
+-14	-18	40	137
+-41	-75	26	138
+-16	-77	34	139
+4	-48	51	140
+-68	-41	-5	141
+35	-67	-34	142
+22	39	39	143
+-56	-13	-10	144
+15	-63	26	145
+-15	4	8	146
+29	-77	25	147
+38	-17	45	148
+23	10	1	149
+66	-8	25	150
+51	-6	32	151
+-39	-75	44	152
+-11	45	8	153
+52	7	-30	154
+-21	41	-20	155
+-12	-95	-13	156
+8	42	-5	157
+34	38	-12	158
+-16	-46	73	159
+37	-84	13	160
+18	-47	-10	161
+-11	-56	16	162
+48	25	27	163
+-53	3	-27	164
+46	16	-30	165
+-31	19	-19	166
+37	-81	1	167
+52	-59	36	168
+27	16	-17	169
+24	45	-15	170
+-44	12	-34	171
+-46	-61	21	172
+-49	-11	35	173
+-25	-98	-12	174
+-33	-79	-13	175
+11	-54	17	176
+23	33	48	177
+-3	-49	13	178
+12	-17	8	179
+-38	-33	17	180
+8	48	-15	181
+-10	39	52	182
+43	-78	-12	183
+20	-29	60	184
+-40	-19	54	185
+-20	45	39	186
+13	30	59	187
+-24	-91	19	188
+-16	29	53	189
+8	-91	-7	190
+-21	-31	61	191
+6	67	-4	192
+17	-80	-34	193
+-23	-30	72	194
+2	-28	60	195
+15	-77	31	196
+3	-17	58	197
+55	-31	-17	198
+-31	-10	-36	199
+-40	-88	-6	200
+-18	63	-9	201
+27	-59	-9	202
+49	-3	-38	203
+-31	-11	-0	204
+65	-24	-19	205
+17	-28	-17	206
+-7	51	-1	207
+24	32	-18	208
+9	54	3	209
+-7	-55	27	210
+-21	-22	-20	211
+34	54	-13	212
+-38	-15	69	213
+-38	-27	69	214
+65	-12	-19	215
+-16	-52	-1	216
+-8	48	23	217
+-3	44	-9	218
+-37	-29	-26	219
+27	-97	-13	220
+17	-91	-14	221
+6	54	16	222
+8	41	-24	223
+8	-48	31	224
+24	-87	24	225
+-58	-26	-15	226
+29	-17	71	227
+-68	-23	-16	228
+-10	-18	7	229
+-13	-17	75	230
+-7	-33	72	231
+15	-87	37	232
+-20	64	19	233
+42	-20	55	234
+26	-79	-16	235
+-10	55	39	236
+13	-33	75	237
+33	-12	-34	238
+-26	-90	3	239
+-7	-21	65	240
+10	-17	74	241
+-44	-65	35	242
+6	-59	35	243
+6	64	22	244
+-18	-68	5	245
+-16	-65	-20	246
+8	-72	11	247
+13	55	38	248
+-14	-91	31	249
+-3	-81	21	250
+20	-86	-2	251
+-50	-7	-39	252
+-56	-45	-24	253
+-8	-81	7	254
+20	-66	2	255
+6	-81	6	256
+52	-34	-27	257
+-15	-72	-8	258
+6	-24	-0	259
+28	-77	-32	260
+22	-58	-23	261
+1	-62	-18	262
+-22	7	-5	263
+-5	-28	-4	264

junifer/data/__init__.py

@@ -8,12 +8,14 @@ from .coordinates import (
     list_coordinates,
     load_coordinates,
     register_coordinates,
+    get_coordinates,
 )
 from .parcellations import (
     list_parcellations,
     load_parcellation,
     register_parcellation,
     merge_parcellations,
+    get_parcellation,
 )
 
 from .masks import (
@@ -23,4 +25,6 @@ from .masks import (
     get_mask,
 )
 
+from .template_spaces import get_template, get_xfm
+
 from . import utils