CerebrA atlas Python

cerebra_atlas_python offers Python

CerebrA is an accurate non-linear registration of cortical and subcortical labelling from Mindboggle 101 to the symmetric MNI-ICBM2009c atlas. cerebra_atlas_python abstracts the following:

cerebra_atlas_python functionality

abstract coordinate frame transformations

https://nist.mni.mcgill.ca/icbm-152-nonlinear-atlases-2009/

Cerebra Atlas

MNIAverage: https://www.dropbox.com/scl/fi/zoff6ihk3711zn6phu2zt/MNIAverage.zip?rlkey=jrg63liehpuhus4suyyfmibuz&dl=0 Cerebra Atlas: https://www.dropbox.com/scl/fi/ivvh2afex6idffmano3qj/10.12751_g-node.be5e62.zip?rlkey=ie3w8lbd5b5377xotsjgnwkrg&dl=0

USAGE / USE CASES

Easily access average brain volume.

Abstract coordinate frames

from cerebra_atlas_python import CerebrA
cerebra = CerebrA()
cerebra.orthoview()

Cerebra Atlas

REQUIREMENTS:

• Python3 + dependencies (TODO)
• Freesurfer (optional)

INSTALL

Tested for Python 3.10.14

Building wheels

$ git clone https://github.com/kdotdot/cerebra_atlas_python.git
$ cd cerebra_atlas_python
$ pip install -r requirements.txt
$ pip install --editable .

COMPUTING BRAIN DATA (optional)

The whole data folder generation (cerebra_data) process is outlined in notebooks/0.0-generate-cerebra-data.ipynb

1. Use Freesurfer to perform cortical reconstruction and generate Boundary Element Model (BEM) surfaces
2. Convert CerebrA volume to T1w scan coordinate frame
3. Process region metadata
4. Manually align fiducials(?)

Data sources:

Original datasets used to build the processed versions of the volumes.

• CerebrA: $CEREBRA_DIR
• ICBM 2009c Nonlinear Symmetric [NIFTI]: $ICBM_DIR

Steps:

1) Use Freesurfer to perform cortical reconstruction and generate Boundary Element Model (BEM) surfaces

• Perform cortical reconstruction from MRI scan using recon-all

$ recon-all -subjid icbm152 -i $ICBM_DIR/mni_icbm152_t1_tal_nlin_sym_09c.nii -all

• Generate boundary element model (BEM) using watershed algoritm
BEM surfaces were generated using the FreeSurfer watershed algorithm through MNE's `mne.bem.make_watershed_bem`
• Manually edit BEM surfaces
BEM surfaces are manually edited so that all inner surfaces are contained within the outer surfaces as explained [here](https://mne.tools/stable/auto_tutorials/forward/80_fix_bem_in_blender.html).

Manual editing of BEM surfaces produced by recon-all

2) Convert CerebrA volume to T1w scan coordinate frame

Convert original .nii into .mgz

CerebrA_in_head.mgz can be computed using Freesurfer and the following commands. Transforms volume from Native anatomical space (193, 229, 193) to Freesurfer space (256, 256, 256):

$ mri_convert $CEREBRA_DIR"/CerebrA.nii" $CEREBRA_DIR"/CerebrA.mgz"

Transform CerebrA volumne into Freesurfer 'head' (head or mri??) coordinate frame (256x256x256)

$ mri_vol2vol --mov $CEREBRA_DIR"/CerebrA.mgz" --o $CEREBRA_DIR"/CerebrA_in_head.mgz" --regheader --targ $SUBJECT_DIR/mri/T1.mgz

3) Process region metadata

	Mindboggle ID	Label Name	CerebrA ID	hemisphere	cortical	color
0	0	Empty	0			#000000
1	2027	Rostral Middle Frontal	1	Right	True	#ff001e
2	631	Vermal lobules VI-VII	2	Right	False	#ff0013
3	2009	Inferior temporal	3	Right	True	#ff0003
4	58	Accumbens Area	4	Right	False	#ff0700
5	44	Inferior Lateral Ventricle	5	Right	False	#ff1700
6	2021	Pericalcarine	6	Right	True	#ff2200
7	2012	Lateral Orbitofrontal	7	Right	True	#ff3200
8	2026	Rostral Anterior Cingulate	8	Right	True	#ff3d00
9	2029	Superior Parietal	9	Right	True	#ff4d00
10	2008	Inferior Parietal	10	Right	True	#ff5800
11	16	Brainstem	11	Right	False	#ff6800
12	2013	Lingual	12	Right	True	#ff7300
13	2022	Postcentral	13	Right	True	#ff8300
14	2034	Transverse Temporal	14	Right	True	#ff8e00
15	2014	Medial Orbitofrontal	15	Right	True	#ff9e00
16	2017	Paracentral	16	Right	True	#ffa900
17	85	Optic Chiasm	17	Right	False	#ffb900
18	2016	Parahippocampal	18	Right	True	#ffc400
19	54	Amygdala	19	Right	False	#ffd400
20	632	Vermal lobules VIII-X	20	Right	False	#ffdf00
21	51	Putamen	21	Right	False	#ffef00
22	2020	Pars Triangularis	22	Right	True	#fffa00
23	2035	Insula	23	Right	True	#f3ff00
24	2007	Fusiform	24	Right	True	#e8ff00
25	92	Basal Forebrain	25	Right	False	#d8ff00
26	60	Ventral Diencephalon	26	Right	False	#cdff00
27	52	Pallidum	27	Right	False	#bdff00
28	2015	Middle Temporal	28	Right	True	#b2ff00
29	14	Third Ventricle	29	Right	False	#a2ff00
30	2002	Caudal Anterior Cingulate	30	Right	True	#97ff00
31	2025	Precuneus	31	Right	True	#87ff00
32	2018	Pars Opercularis	32	Right	True	#7cff00
33	2010	Isthmus Cingulate	33	Right	True	#6cff00
34	2011	Lateral Occipital	34	Right	True	#61ff00
35	2024	Precentral	35	Right	True	#56ff00
36	2006	Entorhinal	36	Right	True	#46ff00
37	15	Fourth Ventricle	37	Right	False	#3bff00
38	2028	Superior Frontal	38	Right	True	#2bff00
39	46	Cerebellum White Matter	39	Right	False	#20ff00
40	49	Thalamus	40	Right	False	#10ff00
41	43	Lateral Ventricle	41	Right	False	#05ff00
42	2003	Caudal Middle Frontal	42	Right	True	#00ff0a
43	2005	Cuneus	43	Right	True	#00ff15
44	2019	Pars Orbitalis	44	Right	True	#00ff25
45	2030	Superior Temporal	45	Right	True	#00ff30
46	45	Cerebellum Gray Matter	46	Right	False	#00ff40
47	2023	Posterior Cingulate	47	Right	True	#00ff4b
48	53	Hippocampus	48	Right	False	#00ff5b
49	50	Caudate	49	Right	False	#00ff66
50	630	Vermal lobules I-V	50	Right	False	#00ff76
51	2031	Supramarginal	51	Right	True	#00ff81
52	1027	Rostral Middle Frontal	52	Left	True	#00ff91
53	631	Vermal lobules VI-VII	53	Left	False	#00ff9b
54	1009	Inferior temporal	54	Left	True	#00ffac
55	58	Accumbens Area	55	Left	False	#00ffb6
56	44	Inferior Lateral Ventricle	56	Left	False	#00ffc6
57	1021	Pericalcarine	57	Left	True	#00ffd1
58	1012	Lateral Orbitofrontal	58	Left	True	#00ffe1
59	1026	Rostral Anterior Cingulate	59	Left	True	#00ffec
60	1029	Superior Parietal	60	Left	True	#00fffc
61	1008	Inferior Parietal	61	Left	True	#00f6ff
62	16	Brainstem	62	Left	False	#00e6ff
63	1013	Lingual	63	Left	True	#00dbff
64	1022	Postcentral	64	Left	True	#00caff
65	1034	Transverse Temporal	65	Left	True	#00c0ff
66	1014	Medial Orbitofrontal	66	Left	True	#00afff
67	1017	Paracentral	67	Left	True	#00a4ff
68	85	Optic Chiasm	68	Left	False	#0094ff
69	1016	Parahippocampal	69	Left	True	#0089ff
70	54	Amygdala	70	Left	False	#007eff
71	632	Vermal lobules VIII-X	71	Left	False	#006eff
72	51	Putamen	72	Left	False	#0063ff
73	1020	Pars Triangularis	73	Left	True	#0053ff
74	1035	Insula	74	Left	True	#0048ff
75	1007	Fusiform	75	Left	True	#0038ff
76	92	Basal Forebrain	76	Left	False	#002dff
77	60	Ventral Diencephalon	77	Left	False	#001dff
78	52	Pallidum	78	Left	False	#0012ff
79	1015	Middle Temporal	79	Left	True	#0001ff
80	14	Third Ventricle	80	Left	False	#0800ff
81	1002	Caudal Anterior Cingulate	81	Left	True	#1900ff
82	1025	Precuneus	82	Left	True	#2400ff
83	1018	Pars Opercularis	83	Left	True	#3400ff
84	1010	Isthmus Cingulate	84	Left	True	#3f00ff
85	1011	Lateral Occipital	85	Left	True	#4f00ff
86	1024	Precentral	86	Left	True	#5a00ff
87	1006	Entorhinal	87	Left	True	#6a00ff
88	15	Fourth Ventricle	88	Left	False	#7500ff
89	1028	Superior Frontal	89	Left	True	#8500ff
90	46	Cerebellum White Matter	90	Left	False	#9000ff
91	49	Thalamus	91	Left	False	#a100ff
92	43	Lateral Ventricle	92	Left	False	#ac00ff
93	1003	Caudal Middle Frontal	93	Left	True	#bc00ff
94	1005	Cuneus	94	Left	True	#c700ff
95	1019	Pars Orbitalis	95	Left	True	#d700ff
96	1030	Superior Temporal	96	Left	True	#e200ff
97	45	Cerebellum Gray Matter	97	Left	False	#f200ff
98	1023	Posterior Cingulate	98	Left	True	#fd00ff
99	53	Hippocampus	99	Left	False	#ff00f0
100	50	Caudate	100	Left	False	#ff00e5
101	630	Vermal lobules I-V	101	Left	False	#ff00d4
102	1031	Supramarginal	102	Left	True	#ff00ca
103	0	White matter	103			#ffdddd

TODOS:

• Update README
• Create documentation page
• Create backup of data sources
• Publish library -> Get DOI -> Create python dependencies file -> Upload to pip