AFNI Preprocessing & Group Analysis

Author: Monika Doerig

Date: May 1 2025

License:

MIT License

Note: If this notebook uses neuroimaging tools from Neurocontainers, those tools retain their original licenses. Please see Neurodesk citation guidelines for details.

Citation:

Tools included in this workflow

AFNI

• Cox RW (1996). AFNI: software for analysis and visualization of functional magnetic resonance neuroimages. Comput Biomed Res 29(3):162-173. doi:10.1006/cbmr.1996.0014

• RW Cox, JS Hyde (1997). Software tools for analysis and visualization of FMRI Data. NMR in Biomedicine, 10: 171-178., https://pubmed.ncbi.nlm.nih.gov/9430344/

Workflows this work is based on

• AFNI Preprocessing

• AFNI Preprocessing and GLM

Educational resources

Andy’s Brain Book:

• This AFNI example is based on the AFNI Tutorial: Statistics and Modeling from Andy’s Brain Book (Jahn, 2022. doi:10.5281/zenodo.5879293)

Dataset

Flanker Dataset from OpenNeuro:

• Kelly AMC and Uddin LQ and Biswal BB and Castellanos FX and Milham MP (2018). Flanker task (event-related). OpenNeuro Dataset ds000102. [Dataset] doi: null

• Kelly AM, Uddin LQ, Biswal BB, Castellanos FX, Milham MP. Competition between functional brain networks mediates behavioral variability. Neuroimage. 2008 Jan 1;39(1):527-37. doi: 10.1016/j.neuroimage.2007.08.008. Epub 2007 Aug 23. PMID: 17919929.

• Mennes, M., Kelly, C., Zuo, X.N., Di Martino, A., Biswal, B.B., Castellanos, F.X., Milham, M.P. (2010). Inter-individual differences in resting-state functional connectivity predict task-induced BOLD activity. Neuroimage, 50(4):1690-701. doi: 10.1016/j.neuroimage.2010.01.002. Epub 2010 Jan 15. Erratum in: Neuroimage. 2011 Mar 1;55(1):434

• Mennes, M., Zuo, X.N., Kelly, C., Di Martino, A., Zang, Y.F., Biswal, B., Castellanos, F.X., Milham, M.P. (2011). Linking inter-individual differences in neural activation and behavior to intrinsic brain dynamics. Neuroimage, 54(4):2950-9. doi: 10.1016/j.neuroimage.2010.10.046ed in your example

Load packages

import module
await module.load('afni/21.2.00')
await module.list()

['afni/21.2.00']

Import Python Modules

%%capture
! pip install nibabel numpy nilearn scipy

import os
from glob import glob
import subprocess
import nibabel as nib
import numpy as np
import matplotlib.pyplot as plt
from nilearn import image, plotting
from ipyniivue import NiiVue
from IPython.display import display, Markdown, Image
from scipy.stats import ttest_1samp
from concurrent.futures import ProcessPoolExecutor, as_completed
from tqdm.notebook import tqdm 

1. Download Data

# 9 subjects from the Flanker Dataset
PATTERN = "sub-0*"
!datalad install https://github.com/OpenNeuroDatasets/ds000102.git
!cd ds000102 && datalad get $PATTERN

action summary:
  get (notneeded: 9)

The data is structured in BIDS format:

!tree -L 4 ds000102

ds000102
├── CHANGES
├── README
├── T1w.json
├── dataset_description.json
├── derivatives
│   └── mriqc
│       ├── aMRIQC.csv -> ../../.git/annex/objects/Q4/jv/MD5E-s14180--3addf0456b803b7c5ec5147481ecdd62.csv/MD5E-s14180--3addf0456b803b7c5ec5147481ecdd62.csv
│       ├── anatomical_group.pdf -> ../../.git/annex/objects/6m/q9/MD5E-s98927--d11151f65ae061833e7fd4373adfec3f.pdf/MD5E-s98927--d11151f65ae061833e7fd4373adfec3f.pdf
│       ├── anatomical_sub-01.pdf -> ../../.git/annex/objects/K3/7x/MD5E-s2747349--5d40f2a54fb4194ac4a79f0295ff51c0.pdf/MD5E-s2747349--5d40f2a54fb4194ac4a79f0295ff51c0.pdf
│       ├── anatomical_sub-02.pdf -> ../../.git/annex/objects/Kx/Kv/MD5E-s2803965--56f6b768362bd9b7f0ef501b8cb6dde6.pdf/MD5E-s2803965--56f6b768362bd9b7f0ef501b8cb6dde6.pdf
│       ├── anatomical_sub-03.pdf -> ../../.git/annex/objects/kx/g5/MD5E-s2809843--e90d7a4859ed4be986b55e23f93ca89d.pdf/MD5E-s2809843--e90d7a4859ed4be986b55e23f93ca89d.pdf
│       ├── anatomical_sub-04.pdf -> ../../.git/annex/objects/JK/Zm/MD5E-s2846770--4869146771178dbb01ac79b95b35a8a1.pdf/MD5E-s2846770--4869146771178dbb01ac79b95b35a8a1.pdf
│       ├── anatomical_sub-05.pdf -> ../../.git/annex/objects/zm/FG/MD5E-s2824086--fda634d34556c83005a5eb2ca8c498dd.pdf/MD5E-s2824086--fda634d34556c83005a5eb2ca8c498dd.pdf
│       ├── anatomical_sub-06.pdf -> ../../.git/annex/objects/92/q0/MD5E-s2798058--fdddf0aff1eca8f61ed7c8b04ada9735.pdf/MD5E-s2798058--fdddf0aff1eca8f61ed7c8b04ada9735.pdf
│       ├── anatomical_sub-07.pdf -> ../../.git/annex/objects/39/3K/MD5E-s2795270--29ce2e2352596df940e5f3fae45b5a38.pdf/MD5E-s2795270--29ce2e2352596df940e5f3fae45b5a38.pdf
│       ├── anatomical_sub-08.pdf -> ../../.git/annex/objects/Fx/F4/MD5E-s2727492--b55dad8ffe22fc035110ecf4119d2960.pdf/MD5E-s2727492--b55dad8ffe22fc035110ecf4119d2960.pdf
│       ├── anatomical_sub-09.pdf -> ../../.git/annex/objects/4M/pz/MD5E-s2887144--28ea830af2a4d741147d18ea9c7fda84.pdf/MD5E-s2887144--28ea830af2a4d741147d18ea9c7fda84.pdf
│       ├── anatomical_sub-10.pdf -> ../../.git/annex/objects/0z/Vw/MD5E-s2874045--6542a57a9fc58f97f2a03c2384663c62.pdf/MD5E-s2874045--6542a57a9fc58f97f2a03c2384663c62.pdf
│       ├── anatomical_sub-11.pdf -> ../../.git/annex/objects/wm/76/MD5E-s2781221--1071b83e3c1b4532879521c37c3329da.pdf/MD5E-s2781221--1071b83e3c1b4532879521c37c3329da.pdf
│       ├── anatomical_sub-12.pdf -> ../../.git/annex/objects/GF/19/MD5E-s2817233--bfd24ca3274fa5efd654e2afd927f9ef.pdf/MD5E-s2817233--bfd24ca3274fa5efd654e2afd927f9ef.pdf
│       ├── anatomical_sub-13.pdf -> ../../.git/annex/objects/9Q/X2/MD5E-s2796088--ed299ab7e1662cb03aa01299eed2602b.pdf/MD5E-s2796088--ed299ab7e1662cb03aa01299eed2602b.pdf
│       ├── anatomical_sub-14.pdf -> ../../.git/annex/objects/Wg/55/MD5E-s2558074--cadc9bd81856dcd02677de84e7e6ca90.pdf/MD5E-s2558074--cadc9bd81856dcd02677de84e7e6ca90.pdf
│       ├── anatomical_sub-15.pdf -> ../../.git/annex/objects/43/Q3/MD5E-s2847293--0c678a4b309d055ad9ba4ba25b77351b.pdf/MD5E-s2847293--0c678a4b309d055ad9ba4ba25b77351b.pdf
│       ├── anatomical_sub-16.pdf -> ../../.git/annex/objects/xq/qj/MD5E-s2890454--87c62253c1711f30d53c41b3ac38dc66.pdf/MD5E-s2890454--87c62253c1711f30d53c41b3ac38dc66.pdf
│       ├── anatomical_sub-17.pdf -> ../../.git/annex/objects/zK/M1/MD5E-s2825765--0a91015e22836a3076641b963e1ccfc6.pdf/MD5E-s2825765--0a91015e22836a3076641b963e1ccfc6.pdf
│       ├── anatomical_sub-18.pdf -> ../../.git/annex/objects/w2/Vk/MD5E-s2821624--1d9a3f0b21ce1f9a3b490d44d36f1f11.pdf/MD5E-s2821624--1d9a3f0b21ce1f9a3b490d44d36f1f11.pdf
│       ├── anatomical_sub-19.pdf -> ../../.git/annex/objects/J2/Jq/MD5E-s2453814--533411f3353cb3fa0264485e81f3fcf6.pdf/MD5E-s2453814--533411f3353cb3fa0264485e81f3fcf6.pdf
│       ├── anatomical_sub-20.pdf -> ../../.git/annex/objects/MF/9X/MD5E-s2881144--176c560778c55db87e8468b3246d373c.pdf/MD5E-s2881144--176c560778c55db87e8468b3246d373c.pdf
│       ├── anatomical_sub-21.pdf -> ../../.git/annex/objects/XQ/p1/MD5E-s2330589--b7546dfe5fb43a974cd23111b860c493.pdf/MD5E-s2330589--b7546dfe5fb43a974cd23111b860c493.pdf
│       ├── anatomical_sub-22.pdf -> ../../.git/annex/objects/Fx/k8/MD5E-s2505165--55f0661ad209b742c517cc5b5469436a.pdf/MD5E-s2505165--55f0661ad209b742c517cc5b5469436a.pdf
│       ├── anatomical_sub-23.pdf -> ../../.git/annex/objects/qj/8K/MD5E-s2784018--7e8697a7d4601547a899a27af132166d.pdf/MD5E-s2784018--7e8697a7d4601547a899a27af132166d.pdf
│       ├── anatomical_sub-24.pdf -> ../../.git/annex/objects/G8/Kw/MD5E-s2828817--e86be931adef2a7b0297d557d827d629.pdf/MD5E-s2828817--e86be931adef2a7b0297d557d827d629.pdf
│       ├── anatomical_sub-25.pdf -> ../../.git/annex/objects/XG/kg/MD5E-s2447908--3d392b9d27929dc4146d2b47be16e8dc.pdf/MD5E-s2447908--3d392b9d27929dc4146d2b47be16e8dc.pdf
│       ├── anatomical_sub-26.pdf -> ../../.git/annex/objects/8P/42/MD5E-s2850007--6d2f87a305b30d5704aaf4be9b8ff1e6.pdf/MD5E-s2850007--6d2f87a305b30d5704aaf4be9b8ff1e6.pdf
│       ├── fMRIQC.csv -> ../../.git/annex/objects/2Z/Ff/MD5E-s21038--cbe73db3db1beb0a1977583cff2a724b.csv/MD5E-s21038--cbe73db3db1beb0a1977583cff2a724b.csv
│       ├── functional_group.pdf -> ../../.git/annex/objects/Kq/xg/MD5E-s90712--7058c3db328fecb86303bc27a9ef0110.pdf/MD5E-s90712--7058c3db328fecb86303bc27a9ef0110.pdf
│       ├── functional_sub-01.pdf -> ../../.git/annex/objects/k2/vQ/MD5E-s1157925--e055f942b72b9aabad7a5e3d7b25b201.pdf/MD5E-s1157925--e055f942b72b9aabad7a5e3d7b25b201.pdf
│       ├── functional_sub-02.pdf -> ../../.git/annex/objects/X3/X6/MD5E-s1235840--cb32b7f8f1274af250b4f0fc15dacecb.pdf/MD5E-s1235840--cb32b7f8f1274af250b4f0fc15dacecb.pdf
│       ├── functional_sub-03.pdf -> ../../.git/annex/objects/Vp/0x/MD5E-s1228507--73ab1cc4cb27712892fcb10a0853ba7c.pdf/MD5E-s1228507--73ab1cc4cb27712892fcb10a0853ba7c.pdf
│       ├── functional_sub-04.pdf -> ../../.git/annex/objects/xk/jz/MD5E-s1252659--8ae6d1b02767c1ddb72dd7e6afefe696.pdf/MD5E-s1252659--8ae6d1b02767c1ddb72dd7e6afefe696.pdf
│       ├── functional_sub-05.pdf -> ../../.git/annex/objects/Zm/VJ/MD5E-s1258815--dd043691d548a501dd63d1aaf420e43c.pdf/MD5E-s1258815--dd043691d548a501dd63d1aaf420e43c.pdf
│       ├── functional_sub-06.pdf -> ../../.git/annex/objects/M5/gq/MD5E-s1247345--9c06bc69792b812ab8deffb01c6656c2.pdf/MD5E-s1247345--9c06bc69792b812ab8deffb01c6656c2.pdf
│       ├── functional_sub-07.pdf -> ../../.git/annex/objects/25/35/MD5E-s1229731--99cc64e99df0025ccb0341cd0dcf688b.pdf/MD5E-s1229731--99cc64e99df0025ccb0341cd0dcf688b.pdf
│       ├── functional_sub-08.pdf -> ../../.git/annex/objects/MX/vQ/MD5E-s1222308--e13c56f17109d3f142c9c4db60fea674.pdf/MD5E-s1222308--e13c56f17109d3f142c9c4db60fea674.pdf
│       ├── functional_sub-09.pdf -> ../../.git/annex/objects/90/0F/MD5E-s1265097--41a69211a0569413917ce3825eac95d6.pdf/MD5E-s1265097--41a69211a0569413917ce3825eac95d6.pdf
│       ├── functional_sub-10.pdf -> ../../.git/annex/objects/FZ/gq/MD5E-s1299358--12ccfc4a5f52b077b99481fe25aa8ef1.pdf/MD5E-s1299358--12ccfc4a5f52b077b99481fe25aa8ef1.pdf
│       ├── functional_sub-11.pdf -> ../../.git/annex/objects/MJ/mQ/MD5E-s1166014--3465ef6b18514d3cd361c0bffe2b73fc.pdf/MD5E-s1166014--3465ef6b18514d3cd361c0bffe2b73fc.pdf
│       ├── functional_sub-12.pdf -> ../../.git/annex/objects/xp/1f/MD5E-s1177325--6fe4937d5aa567fb5b3c3977362fc9af.pdf/MD5E-s1177325--6fe4937d5aa567fb5b3c3977362fc9af.pdf
│       ├── functional_sub-13.pdf -> ../../.git/annex/objects/4g/vW/MD5E-s1178873--96f341322d21e2bdeb709edc5b047df0.pdf/MD5E-s1178873--96f341322d21e2bdeb709edc5b047df0.pdf
│       ├── functional_sub-14.pdf -> ../../.git/annex/objects/5p/6X/MD5E-s1206987--729f64cf514c9103556c53ccb5430bc4.pdf/MD5E-s1206987--729f64cf514c9103556c53ccb5430bc4.pdf
│       ├── functional_sub-15.pdf -> ../../.git/annex/objects/m1/k9/MD5E-s1223617--9239a1c2d968ed18093b69d28fd9e654.pdf/MD5E-s1223617--9239a1c2d968ed18093b69d28fd9e654.pdf
│       ├── functional_sub-16.pdf -> ../../.git/annex/objects/jq/wP/MD5E-s1294856--5eb7ec97924a22c7e68fd95373694e7e.pdf/MD5E-s1294856--5eb7ec97924a22c7e68fd95373694e7e.pdf
│       ├── functional_sub-17.pdf -> ../../.git/annex/objects/0m/3Q/MD5E-s1238563--129db424a50b7889278024828c08c736.pdf/MD5E-s1238563--129db424a50b7889278024828c08c736.pdf
│       ├── functional_sub-18.pdf -> ../../.git/annex/objects/VF/Fm/MD5E-s1197868--3b23e8d53b11d98d49b1adf62ff559df.pdf/MD5E-s1197868--3b23e8d53b11d98d49b1adf62ff559df.pdf
│       ├── functional_sub-19.pdf -> ../../.git/annex/objects/Jj/m8/MD5E-s1164028--aea7dfa78e9be2e83a9b313f2ebdc4bd.pdf/MD5E-s1164028--aea7dfa78e9be2e83a9b313f2ebdc4bd.pdf
│       ├── functional_sub-20.pdf -> ../../.git/annex/objects/x1/ZQ/MD5E-s1292308--8869b1b640797a2be2aa03be69b89840.pdf/MD5E-s1292308--8869b1b640797a2be2aa03be69b89840.pdf
│       ├── functional_sub-21.pdf -> ../../.git/annex/objects/MG/zW/MD5E-s1216271--3d5c5ca0f8f4ba06b3289e197a40defd.pdf/MD5E-s1216271--3d5c5ca0f8f4ba06b3289e197a40defd.pdf
│       ├── functional_sub-22.pdf -> ../../.git/annex/objects/5m/pj/MD5E-s1142289--4f9e57d8bfe3d39881c43b959189d69f.pdf/MD5E-s1142289--4f9e57d8bfe3d39881c43b959189d69f.pdf
│       ├── functional_sub-23.pdf -> ../../.git/annex/objects/m7/Z2/MD5E-s1233046--7758914aecbf2b5d01cd0825952609be.pdf/MD5E-s1233046--7758914aecbf2b5d01cd0825952609be.pdf
│       ├── functional_sub-24.pdf -> ../../.git/annex/objects/mz/5m/MD5E-s1265224--c188bd88fc1c99308389f528ea4df71e.pdf/MD5E-s1265224--c188bd88fc1c99308389f528ea4df71e.pdf
│       ├── functional_sub-25.pdf -> ../../.git/annex/objects/Mk/G6/MD5E-s1260984--1b16abcbbf55ccc7763f1d704d76628f.pdf/MD5E-s1260984--1b16abcbbf55ccc7763f1d704d76628f.pdf
│       └── functional_sub-26.pdf -> ../../.git/annex/objects/1m/zq/MD5E-s1285726--6838f727d5c4b5593a7b5e0e6b20483a.pdf/MD5E-s1285726--6838f727d5c4b5593a7b5e0e6b20483a.pdf
├── make_Timings.sh
├── participants.tsv
├── sub-01
│   ├── anat
│   │   └── sub-01_T1w.nii.gz -> ../../.git/annex/objects/Pf/6k/MD5E-s10581116--757e697a01eeea5c97a7d6fbc7153373.nii.gz/MD5E-s10581116--757e697a01eeea5c97a7d6fbc7153373.nii.gz
│   └── func
│       ├── congruent.1D
│       ├── congruent_run1.txt
│       ├── congruent_run2.txt
│       ├── incongruent.1D
│       ├── incongruent_run1.txt
│       ├── incongruent_run2.txt
│       ├── sub-01_task-flanker_run-1_bold.nii.gz -> ../../.git/annex/objects/5m/w9/MD5E-s28061534--8e8c44ff53f9b5d46f2caae5916fa4ef.nii.gz/MD5E-s28061534--8e8c44ff53f9b5d46f2caae5916fa4ef.nii.gz
│       ├── sub-01_task-flanker_run-1_events.tsv
│       ├── sub-01_task-flanker_run-2_bold.nii.gz -> ../../.git/annex/objects/2F/58/MD5E-s28143286--f0bcf782c3688e2cf7149b4665949484.nii.gz/MD5E-s28143286--f0bcf782c3688e2cf7149b4665949484.nii.gz
│       └── sub-01_task-flanker_run-2_events.tsv
├── sub-02
│   ├── anat
│   │   └── sub-02_T1w.nii.gz -> ../../.git/annex/objects/3m/FF/MD5E-s10737123--cbd4181ee26559e8ec0a441fa2f834a7.nii.gz/MD5E-s10737123--cbd4181ee26559e8ec0a441fa2f834a7.nii.gz
│   └── func
│       ├── congruent.1D
│       ├── congruent_run1.txt
│       ├── congruent_run2.txt
│       ├── incongruent.1D
│       ├── incongruent_run1.txt
│       ├── incongruent_run2.txt
│       ├── sub-02_task-flanker_run-1_bold.nii.gz -> ../../.git/annex/objects/8v/2j/MD5E-s29188378--80050f0deb13562c24f2fc23f8d095bd.nii.gz/MD5E-s29188378--80050f0deb13562c24f2fc23f8d095bd.nii.gz
│       ├── sub-02_task-flanker_run-1_events.tsv
│       ├── sub-02_task-flanker_run-2_bold.nii.gz -> ../../.git/annex/objects/fM/Kw/MD5E-s29193540--cc013f2d7d148b448edca8aada349d02.nii.gz/MD5E-s29193540--cc013f2d7d148b448edca8aada349d02.nii.gz
│       └── sub-02_task-flanker_run-2_events.tsv
├── sub-03
│   ├── anat
│   │   └── sub-03_T1w.nii.gz -> ../../.git/annex/objects/7W/9z/MD5E-s10707026--8f1858934cc7c7457e3a4a71cc2131fc.nii.gz/MD5E-s10707026--8f1858934cc7c7457e3a4a71cc2131fc.nii.gz
│   └── func
│       ├── congruent.1D
│       ├── congruent_run1.txt
│       ├── congruent_run2.txt
│       ├── incongruent.1D
│       ├── incongruent_run1.txt
│       ├── incongruent_run2.txt
│       ├── sub-03_task-flanker_run-1_bold.nii.gz -> ../../.git/annex/objects/q6/kF/MD5E-s28755729--b19466702eee6b9385bd6e19e362f94c.nii.gz/MD5E-s28755729--b19466702eee6b9385bd6e19e362f94c.nii.gz
│       ├── sub-03_task-flanker_run-1_events.tsv
│       ├── sub-03_task-flanker_run-2_bold.nii.gz -> ../../.git/annex/objects/zV/K1/MD5E-s28782544--8d9700a435d08c90f0c1d534efdc8b69.nii.gz/MD5E-s28782544--8d9700a435d08c90f0c1d534efdc8b69.nii.gz
│       └── sub-03_task-flanker_run-2_events.tsv
├── sub-04
│   ├── anat
│   │   └── sub-04_T1w.nii.gz -> ../../.git/annex/objects/FW/14/MD5E-s10738444--2a9a2ba4ea7d2324c84bf5a2882f196c.nii.gz/MD5E-s10738444--2a9a2ba4ea7d2324c84bf5a2882f196c.nii.gz
│   └── func
│       ├── congruent.1D
│       ├── congruent_run1.txt
│       ├── congruent_run2.txt
│       ├── incongruent.1D
│       ├── incongruent_run1.txt
│       ├── incongruent_run2.txt
│       ├── sub-04_task-flanker_run-1_bold.nii.gz -> ../../.git/annex/objects/9Z/0Q/MD5E-s29062799--27171406951ea275cb5857ea0dc32345.nii.gz/MD5E-s29062799--27171406951ea275cb5857ea0dc32345.nii.gz
│       ├── sub-04_task-flanker_run-1_events.tsv
│       ├── sub-04_task-flanker_run-2_bold.nii.gz -> ../../.git/annex/objects/FW/FZ/MD5E-s29071279--f89b61fe3ebab26df1374f2564bd95c2.nii.gz/MD5E-s29071279--f89b61fe3ebab26df1374f2564bd95c2.nii.gz
│       └── sub-04_task-flanker_run-2_events.tsv
├── sub-05
│   ├── anat
│   │   └── sub-05_T1w.nii.gz -> ../../.git/annex/objects/k2/Kj/MD5E-s10753867--c4b5788da5f4c627f0f5862da5f46c35.nii.gz/MD5E-s10753867--c4b5788da5f4c627f0f5862da5f46c35.nii.gz
│   └── func
│       ├── congruent.1D
│       ├── congruent_run1.txt
│       ├── congruent_run2.txt
│       ├── incongruent.1D
│       ├── incongruent_run1.txt
│       ├── incongruent_run2.txt
│       ├── sub-05_task-flanker_run-1_bold.nii.gz -> ../../.git/annex/objects/VZ/z5/MD5E-s29667270--0ce9ac78b6aa9a77fc94c655a6ff5a06.nii.gz/MD5E-s29667270--0ce9ac78b6aa9a77fc94c655a6ff5a06.nii.gz
│       ├── sub-05_task-flanker_run-1_events.tsv
│       ├── sub-05_task-flanker_run-2_bold.nii.gz -> ../../.git/annex/objects/z7/MP/MD5E-s29660544--752750dabb21e2cf28e87d1d550a71b9.nii.gz/MD5E-s29660544--752750dabb21e2cf28e87d1d550a71b9.nii.gz
│       └── sub-05_task-flanker_run-2_events.tsv
├── sub-06
│   ├── anat
│   │   └── sub-06_T1w.nii.gz -> ../../.git/annex/objects/5w/G0/MD5E-s10620585--1132eab3830fe59b8a10b6582bb49004.nii.gz/MD5E-s10620585--1132eab3830fe59b8a10b6582bb49004.nii.gz
│   └── func
│       ├── congruent.1D
│       ├── congruent_run1.txt
│       ├── congruent_run2.txt
│       ├── incongruent.1D
│       ├── incongruent_run1.txt
│       ├── incongruent_run2.txt
│       ├── sub-06_task-flanker_run-1_bold.nii.gz -> ../../.git/annex/objects/3x/qj/MD5E-s29386982--e671c0c647ce7d0d4596e35b702ee970.nii.gz/MD5E-s29386982--e671c0c647ce7d0d4596e35b702ee970.nii.gz
│       ├── sub-06_task-flanker_run-1_events.tsv
│       ├── sub-06_task-flanker_run-2_bold.nii.gz -> ../../.git/annex/objects/9j/6P/MD5E-s29379265--e513a2746d2b5c603f96044cf48c557c.nii.gz/MD5E-s29379265--e513a2746d2b5c603f96044cf48c557c.nii.gz
│       └── sub-06_task-flanker_run-2_events.tsv
├── sub-07
│   ├── anat
│   │   └── sub-07_T1w.nii.gz -> ../../.git/annex/objects/08/fF/MD5E-s10718092--38481fbc489dfb1ec4b174b57591a074.nii.gz/MD5E-s10718092--38481fbc489dfb1ec4b174b57591a074.nii.gz
│   └── func
│       ├── congruent.1D
│       ├── congruent_run1.txt
│       ├── congruent_run2.txt
│       ├── incongruent.1D
│       ├── incongruent_run1.txt
│       ├── incongruent_run2.txt
│       ├── sub-07_task-flanker_run-1_bold.nii.gz -> ../../.git/annex/objects/z1/7W/MD5E-s28946009--5baf7a314874b280543fc0f91f2731af.nii.gz/MD5E-s28946009--5baf7a314874b280543fc0f91f2731af.nii.gz
│       ├── sub-07_task-flanker_run-1_events.tsv
│       ├── sub-07_task-flanker_run-2_bold.nii.gz -> ../../.git/annex/objects/Jf/W7/MD5E-s28960603--682e13963bfc49cc6ae05e9ba5c62619.nii.gz/MD5E-s28960603--682e13963bfc49cc6ae05e9ba5c62619.nii.gz
│       └── sub-07_task-flanker_run-2_events.tsv
├── sub-08
│   ├── anat
│   │   └── sub-08_T1w.nii.gz -> ../../.git/annex/objects/mw/MM/MD5E-s10561256--b94dddd8dc1c146aa8cd97f8d9994146.nii.gz/MD5E-s10561256--b94dddd8dc1c146aa8cd97f8d9994146.nii.gz
│   └── func
│       ├── congruent.1D
│       ├── congruent_run1.txt
│       ├── congruent_run2.txt
│       ├── incongruent.1D
│       ├── incongruent_run1.txt
│       ├── incongruent_run2.txt
│       ├── sub-08_task-flanker_run-1_bold.nii.gz -> ../../.git/annex/objects/zX/v9/MD5E-s28641609--47314e6d1a14b8545686110b5b67f8b8.nii.gz/MD5E-s28641609--47314e6d1a14b8545686110b5b67f8b8.nii.gz
│       ├── sub-08_task-flanker_run-1_events.tsv
│       ├── sub-08_task-flanker_run-2_bold.nii.gz -> ../../.git/annex/objects/WZ/F0/MD5E-s28636310--4535bf26281e1c5556ad0d3468e7fe4e.nii.gz/MD5E-s28636310--4535bf26281e1c5556ad0d3468e7fe4e.nii.gz
│       └── sub-08_task-flanker_run-2_events.tsv
├── sub-09
│   ├── anat
│   │   └── sub-09_T1w.nii.gz -> ../../.git/annex/objects/QJ/ZZ/MD5E-s10775967--e6a18e64bc0a6b17254a9564cf9b8f82.nii.gz/MD5E-s10775967--e6a18e64bc0a6b17254a9564cf9b8f82.nii.gz
│   └── func
│       ├── congruent.1D
│       ├── congruent_run1.txt
│       ├── congruent_run2.txt
│       ├── incongruent.1D
│       ├── incongruent_run1.txt
│       ├── incongruent_run2.txt
│       ├── sub-09_task-flanker_run-1_bold.nii.gz -> ../../.git/annex/objects/k9/1X/MD5E-s29200533--59e86a903e0ab3d1d320c794ba1f0777.nii.gz/MD5E-s29200533--59e86a903e0ab3d1d320c794ba1f0777.nii.gz
│       ├── sub-09_task-flanker_run-1_events.tsv
│       ├── sub-09_task-flanker_run-2_bold.nii.gz -> ../../.git/annex/objects/W3/94/MD5E-s29223017--7f3fb9e260d3bd28e29b0b586ce4c344.nii.gz/MD5E-s29223017--7f3fb9e260d3bd28e29b0b586ce4c344.nii.gz
│       └── sub-09_task-flanker_run-2_events.tsv
├── sub-10
│   ├── anat
│   │   └── sub-10_T1w.nii.gz -> ../../.git/annex/objects/5F/3f/MD5E-s10750712--bde2309077bffe22cb65e42ebdce5bfa.nii.gz/MD5E-s10750712--bde2309077bffe22cb65e42ebdce5bfa.nii.gz
│   └── func
│       ├── congruent.1D
│       ├── congruent_run1.txt
│       ├── congruent_run2.txt
│       ├── incongruent.1D
│       ├── incongruent_run1.txt
│       ├── incongruent_run2.txt
│       ├── sub-10_task-flanker_run-1_bold.nii.gz -> ../../.git/annex/objects/3p/qp/MD5E-s29732696--339715d5cec387f4d44dfe94f304a429.nii.gz/MD5E-s29732696--339715d5cec387f4d44dfe94f304a429.nii.gz
│       ├── sub-10_task-flanker_run-1_events.tsv
│       ├── sub-10_task-flanker_run-2_bold.nii.gz -> ../../.git/annex/objects/11/Zx/MD5E-s29724034--16f2bf452524a315182f188becc1866d.nii.gz/MD5E-s29724034--16f2bf452524a315182f188becc1866d.nii.gz
│       └── sub-10_task-flanker_run-2_events.tsv
├── sub-11
│   ├── anat
│   │   └── sub-11_T1w.nii.gz -> ../../.git/annex/objects/kj/xX/MD5E-s10534963--9e5bff7ec0b5df2850e1d05b1af281ba.nii.gz/MD5E-s10534963--9e5bff7ec0b5df2850e1d05b1af281ba.nii.gz
│   └── func
│       ├── congruent.1D
│       ├── congruent_run1.txt
│       ├── congruent_run2.txt
│       ├── incongruent.1D
│       ├── incongruent_run1.txt
│       ├── incongruent_run2.txt
│       ├── sub-11_task-flanker_run-1_bold.nii.gz -> ../../.git/annex/objects/35/fk/MD5E-s28226875--d5012074c2c7a0a394861b010bcf9a8f.nii.gz/MD5E-s28226875--d5012074c2c7a0a394861b010bcf9a8f.nii.gz
│       ├── sub-11_task-flanker_run-1_events.tsv
│       ├── sub-11_task-flanker_run-2_bold.nii.gz -> ../../.git/annex/objects/j7/ff/MD5E-s28198976--c0a64e3b549568c44bb40b1588027c9a.nii.gz/MD5E-s28198976--c0a64e3b549568c44bb40b1588027c9a.nii.gz
│       └── sub-11_task-flanker_run-2_events.tsv
├── sub-12
│   ├── anat
│   │   └── sub-12_T1w.nii.gz -> ../../.git/annex/objects/kx/2F/MD5E-s10550168--a7f651adc817b6678148b575654532a4.nii.gz/MD5E-s10550168--a7f651adc817b6678148b575654532a4.nii.gz
│   └── func
│       ├── congruent.1D
│       ├── congruent_run1.txt
│       ├── congruent_run2.txt
│       ├── incongruent.1D
│       ├── incongruent_run1.txt
│       ├── incongruent_run2.txt
│       ├── sub-12_task-flanker_run-1_bold.nii.gz -> ../../.git/annex/objects/M0/fX/MD5E-s28403807--f1c3eb2e519020f4315a696ea845fc01.nii.gz/MD5E-s28403807--f1c3eb2e519020f4315a696ea845fc01.nii.gz
│       ├── sub-12_task-flanker_run-1_events.tsv
│       ├── sub-12_task-flanker_run-2_bold.nii.gz -> ../../.git/annex/objects/vW/V0/MD5E-s28424992--8740628349be3c056a0411bf4a852b25.nii.gz/MD5E-s28424992--8740628349be3c056a0411bf4a852b25.nii.gz
│       └── sub-12_task-flanker_run-2_events.tsv
├── sub-13
│   ├── anat
│   │   └── sub-13_T1w.nii.gz -> ../../.git/annex/objects/wM/Xw/MD5E-s10609761--440413c3251d182086105649164222c6.nii.gz/MD5E-s10609761--440413c3251d182086105649164222c6.nii.gz
│   └── func
│       ├── congruent.1D
│       ├── congruent_run1.txt
│       ├── congruent_run2.txt
│       ├── incongruent.1D
│       ├── incongruent_run1.txt
│       ├── incongruent_run2.txt
│       ├── sub-13_task-flanker_run-1_bold.nii.gz -> ../../.git/annex/objects/mf/M4/MD5E-s28180916--aa35f4ad0cf630d6396a8a2dd1f3dda6.nii.gz/MD5E-s28180916--aa35f4ad0cf630d6396a8a2dd1f3dda6.nii.gz
│       ├── sub-13_task-flanker_run-1_events.tsv
│       ├── sub-13_task-flanker_run-2_bold.nii.gz -> ../../.git/annex/objects/XP/76/MD5E-s28202786--8caf1ac548c87b2b35f85e8ae2bf72c1.nii.gz/MD5E-s28202786--8caf1ac548c87b2b35f85e8ae2bf72c1.nii.gz
│       └── sub-13_task-flanker_run-2_events.tsv
├── sub-14
│   ├── anat
│   │   └── sub-14_T1w.nii.gz -> ../../.git/annex/objects/Zw/0z/MD5E-s9223596--33abfb5da565f3487e3a7aebc15f940c.nii.gz/MD5E-s9223596--33abfb5da565f3487e3a7aebc15f940c.nii.gz
│   └── func
│       ├── congruent.1D
│       ├── congruent_run1.txt
│       ├── congruent_run2.txt
│       ├── incongruent.1D
│       ├── incongruent_run1.txt
│       ├── incongruent_run2.txt
│       ├── sub-14_task-flanker_run-1_bold.nii.gz -> ../../.git/annex/objects/Jp/29/MD5E-s29001492--250f1e4daa9be1d95e06af0d56629cc9.nii.gz/MD5E-s29001492--250f1e4daa9be1d95e06af0d56629cc9.nii.gz
│       ├── sub-14_task-flanker_run-1_events.tsv
│       ├── sub-14_task-flanker_run-2_bold.nii.gz -> ../../.git/annex/objects/PK/V2/MD5E-s29068193--5621a3b0af8132c509420b4ad9aaf8fb.nii.gz/MD5E-s29068193--5621a3b0af8132c509420b4ad9aaf8fb.nii.gz
│       └── sub-14_task-flanker_run-2_events.tsv
├── sub-15
│   ├── anat
│   │   └── sub-15_T1w.nii.gz -> ../../.git/annex/objects/Mz/qq/MD5E-s10752891--ddd2622f115ec0d29a0c7ab2366f6f95.nii.gz/MD5E-s10752891--ddd2622f115ec0d29a0c7ab2366f6f95.nii.gz
│   └── func
│       ├── congruent.1D
│       ├── congruent_run1.txt
│       ├── congruent_run2.txt
│       ├── incongruent.1D
│       ├── incongruent_run1.txt
│       ├── incongruent_run2.txt
│       ├── sub-15_task-flanker_run-1_bold.nii.gz -> ../../.git/annex/objects/08/JJ/MD5E-s28285239--feda22c4526af1910fcee58d4c42f07e.nii.gz/MD5E-s28285239--feda22c4526af1910fcee58d4c42f07e.nii.gz
│       ├── sub-15_task-flanker_run-1_events.tsv
│       ├── sub-15_task-flanker_run-2_bold.nii.gz -> ../../.git/annex/objects/9f/0W/MD5E-s28289760--433000a1def662e72d8433dba151c61b.nii.gz/MD5E-s28289760--433000a1def662e72d8433dba151c61b.nii.gz
│       └── sub-15_task-flanker_run-2_events.tsv
├── sub-16
│   ├── anat
│   │   └── sub-16_T1w.nii.gz -> ../../.git/annex/objects/4g/8k/MD5E-s10927450--a196f7075c793328dd6ff3cebf36ea6b.nii.gz/MD5E-s10927450--a196f7075c793328dd6ff3cebf36ea6b.nii.gz
│   └── func
│       ├── congruent.1D
│       ├── congruent_run1.txt
│       ├── congruent_run2.txt
│       ├── incongruent.1D
│       ├── incongruent_run1.txt
│       ├── incongruent_run2.txt
│       ├── sub-16_task-flanker_run-1_bold.nii.gz -> ../../.git/annex/objects/9z/g2/MD5E-s29757991--1a1648b2fa6cc74e31c94f109d8137ba.nii.gz/MD5E-s29757991--1a1648b2fa6cc74e31c94f109d8137ba.nii.gz
│       ├── sub-16_task-flanker_run-1_events.tsv
│       ├── sub-16_task-flanker_run-2_bold.nii.gz -> ../../.git/annex/objects/k8/4F/MD5E-s29773832--fe08739ea816254395b985ee704aaa99.nii.gz/MD5E-s29773832--fe08739ea816254395b985ee704aaa99.nii.gz
│       └── sub-16_task-flanker_run-2_events.tsv
├── sub-17
│   ├── anat
│   │   └── sub-17_T1w.nii.gz -> ../../.git/annex/objects/jQ/MQ/MD5E-s10826014--8e2a6b062df4d1c4327802f2b905ef36.nii.gz/MD5E-s10826014--8e2a6b062df4d1c4327802f2b905ef36.nii.gz
│   └── func
│       ├── congruent.1D
│       ├── congruent_run1.txt
│       ├── congruent_run2.txt
│       ├── incongruent.1D
│       ├── incongruent_run1.txt
│       ├── incongruent_run2.txt
│       ├── sub-17_task-flanker_run-1_bold.nii.gz -> ../../.git/annex/objects/Wz/2P/MD5E-s28991563--9845f461a017a39d1f6e18baaa0c9c41.nii.gz/MD5E-s28991563--9845f461a017a39d1f6e18baaa0c9c41.nii.gz
│       ├── sub-17_task-flanker_run-1_events.tsv
│       ├── sub-17_task-flanker_run-2_bold.nii.gz -> ../../.git/annex/objects/jF/3m/MD5E-s29057821--84ccc041163bcc5b3a9443951e2a5a78.nii.gz/MD5E-s29057821--84ccc041163bcc5b3a9443951e2a5a78.nii.gz
│       └── sub-17_task-flanker_run-2_events.tsv
├── sub-18
│   ├── anat
│   │   └── sub-18_T1w.nii.gz -> ../../.git/annex/objects/3v/pK/MD5E-s10571510--6fc4b5792bc50ea4d14eb5247676fafe.nii.gz/MD5E-s10571510--6fc4b5792bc50ea4d14eb5247676fafe.nii.gz
│   └── func
│       ├── congruent.1D
│       ├── congruent_run1.txt
│       ├── congruent_run2.txt
│       ├── incongruent.1D
│       ├── incongruent_run1.txt
│       ├── incongruent_run2.txt
│       ├── sub-18_task-flanker_run-1_bold.nii.gz -> ../../.git/annex/objects/94/P2/MD5E-s28185776--5b3879ec6fc4bbe1e48efc64984f88cf.nii.gz/MD5E-s28185776--5b3879ec6fc4bbe1e48efc64984f88cf.nii.gz
│       ├── sub-18_task-flanker_run-1_events.tsv
│       ├── sub-18_task-flanker_run-2_bold.nii.gz -> ../../.git/annex/objects/qp/6K/MD5E-s28234699--58019d798a133e5d7806569374dd8160.nii.gz/MD5E-s28234699--58019d798a133e5d7806569374dd8160.nii.gz
│       └── sub-18_task-flanker_run-2_events.tsv
├── sub-19
│   ├── anat
│   │   └── sub-19_T1w.nii.gz -> ../../.git/annex/objects/Zw/p8/MD5E-s8861893--d338005753d8af3f3d7bd8dc293e2a97.nii.gz/MD5E-s8861893--d338005753d8af3f3d7bd8dc293e2a97.nii.gz
│   └── func
│       ├── congruent.1D
│       ├── congruent_run1.txt
│       ├── congruent_run2.txt
│       ├── incongruent.1D
│       ├── incongruent_run1.txt
│       ├── incongruent_run2.txt
│       ├── sub-19_task-flanker_run-1_bold.nii.gz -> ../../.git/annex/objects/04/k6/MD5E-s28178448--3874e748258cf19aa69a05a7c37ad137.nii.gz/MD5E-s28178448--3874e748258cf19aa69a05a7c37ad137.nii.gz
│       ├── sub-19_task-flanker_run-1_events.tsv
│       ├── sub-19_task-flanker_run-2_bold.nii.gz -> ../../.git/annex/objects/mz/P4/MD5E-s28190932--91e6b3e4318ca28f01de8cb967cf8421.nii.gz/MD5E-s28190932--91e6b3e4318ca28f01de8cb967cf8421.nii.gz
│       └── sub-19_task-flanker_run-2_events.tsv
├── sub-20
│   ├── anat
│   │   └── sub-20_T1w.nii.gz -> ../../.git/annex/objects/g1/FF/MD5E-s11025608--5929806a7aa5720fc755687e1450b06c.nii.gz/MD5E-s11025608--5929806a7aa5720fc755687e1450b06c.nii.gz
│   └── func
│       ├── congruent.1D
│       ├── congruent_run1.txt
│       ├── congruent_run2.txt
│       ├── incongruent.1D
│       ├── incongruent_run1.txt
│       ├── incongruent_run2.txt
│       ├── sub-20_task-flanker_run-1_bold.nii.gz -> ../../.git/annex/objects/v5/ZJ/MD5E-s29931631--bf9abb057367ce66961f0b7913e8e707.nii.gz/MD5E-s29931631--bf9abb057367ce66961f0b7913e8e707.nii.gz
│       ├── sub-20_task-flanker_run-1_events.tsv
│       ├── sub-20_task-flanker_run-2_bold.nii.gz -> ../../.git/annex/objects/J3/KW/MD5E-s29945590--96cfd5b77cd096f6c6a3530015fea32d.nii.gz/MD5E-s29945590--96cfd5b77cd096f6c6a3530015fea32d.nii.gz
│       └── sub-20_task-flanker_run-2_events.tsv
├── sub-21
│   ├── anat
│   │   └── sub-21_T1w.nii.gz -> ../../.git/annex/objects/K6/6K/MD5E-s8662805--77b262ddd929fa08d78591bfbe558ac6.nii.gz/MD5E-s8662805--77b262ddd929fa08d78591bfbe558ac6.nii.gz
│   └── func
│       ├── congruent.1D
│       ├── congruent_run1.txt
│       ├── congruent_run2.txt
│       ├── incongruent.1D
│       ├── incongruent_run1.txt
│       ├── incongruent_run2.txt
│       ├── sub-21_task-flanker_run-1_bold.nii.gz -> ../../.git/annex/objects/Wz/p9/MD5E-s28756041--9ae556d4e3042532d25af5dc4ab31840.nii.gz/MD5E-s28756041--9ae556d4e3042532d25af5dc4ab31840.nii.gz
│       ├── sub-21_task-flanker_run-1_events.tsv
│       ├── sub-21_task-flanker_run-2_bold.nii.gz -> ../../.git/annex/objects/xF/M3/MD5E-s28758438--81866411fc6b6333ec382a20ff0be718.nii.gz/MD5E-s28758438--81866411fc6b6333ec382a20ff0be718.nii.gz
│       └── sub-21_task-flanker_run-2_events.tsv
├── sub-22
│   ├── anat
│   │   └── sub-22_T1w.nii.gz -> ../../.git/annex/objects/JG/ZV/MD5E-s9282392--9e7296a6a5b68df46b77836182b6681a.nii.gz/MD5E-s9282392--9e7296a6a5b68df46b77836182b6681a.nii.gz
│   └── func
│       ├── congruent.1D
│       ├── congruent_run1.txt
│       ├── congruent_run2.txt
│       ├── incongruent.1D
│       ├── incongruent_run1.txt
│       ├── incongruent_run2.txt
│       ├── sub-22_task-flanker_run-1_bold.nii.gz -> ../../.git/annex/objects/qW/Gw/MD5E-s28002098--c6bea10177a38667ceea3261a642b3c6.nii.gz/MD5E-s28002098--c6bea10177a38667ceea3261a642b3c6.nii.gz
│       ├── sub-22_task-flanker_run-1_events.tsv
│       ├── sub-22_task-flanker_run-2_bold.nii.gz -> ../../.git/annex/objects/VX/Zj/MD5E-s28027568--b34d0df9ad62485aba25296939429885.nii.gz/MD5E-s28027568--b34d0df9ad62485aba25296939429885.nii.gz
│       └── sub-22_task-flanker_run-2_events.tsv
├── sub-23
│   ├── anat
│   │   └── sub-23_T1w.nii.gz -> ../../.git/annex/objects/4Z/4x/MD5E-s10626062--db5a6ba6730b319c6425f2e847ce9b14.nii.gz/MD5E-s10626062--db5a6ba6730b319c6425f2e847ce9b14.nii.gz
│   └── func
│       ├── congruent.1D
│       ├── congruent_run1.txt
│       ├── congruent_run2.txt
│       ├── incongruent.1D
│       ├── incongruent_run1.txt
│       ├── incongruent_run2.txt
│       ├── sub-23_task-flanker_run-1_bold.nii.gz -> ../../.git/annex/objects/VK/8F/MD5E-s28965005--4a9a96d9322563510ca14439e7fd6cea.nii.gz/MD5E-s28965005--4a9a96d9322563510ca14439e7fd6cea.nii.gz
│       ├── sub-23_task-flanker_run-1_events.tsv
│       ├── sub-23_task-flanker_run-2_bold.nii.gz -> ../../.git/annex/objects/56/20/MD5E-s29050413--753b0d2c23c4af6592501219c2e2c6bd.nii.gz/MD5E-s29050413--753b0d2c23c4af6592501219c2e2c6bd.nii.gz
│       └── sub-23_task-flanker_run-2_events.tsv
├── sub-24
│   ├── anat
│   │   └── sub-24_T1w.nii.gz -> ../../.git/annex/objects/jQ/fV/MD5E-s10739691--458f0046eff18ee8c43456637766a819.nii.gz/MD5E-s10739691--458f0046eff18ee8c43456637766a819.nii.gz
│   └── func
│       ├── congruent.1D
│       ├── congruent_run1.txt
│       ├── congruent_run2.txt
│       ├── incongruent.1D
│       ├── incongruent_run1.txt
│       ├── incongruent_run2.txt
│       ├── sub-24_task-flanker_run-1_bold.nii.gz -> ../../.git/annex/objects/km/fV/MD5E-s29354610--29ebfa60e52d49f7dac6814cb5fdc2bc.nii.gz/MD5E-s29354610--29ebfa60e52d49f7dac6814cb5fdc2bc.nii.gz
│       ├── sub-24_task-flanker_run-1_events.tsv
│       ├── sub-24_task-flanker_run-2_bold.nii.gz -> ../../.git/annex/objects/Wj/KK/MD5E-s29423307--fedaa1d7c6e34420735bb3bbe5a2fe38.nii.gz/MD5E-s29423307--fedaa1d7c6e34420735bb3bbe5a2fe38.nii.gz
│       └── sub-24_task-flanker_run-2_events.tsv
├── sub-25
│   ├── anat
│   │   └── sub-25_T1w.nii.gz -> ../../.git/annex/objects/Gk/FQ/MD5E-s8998578--f560d832f13e757b485c16d570bf6ebc.nii.gz/MD5E-s8998578--f560d832f13e757b485c16d570bf6ebc.nii.gz
│   └── func
│       ├── congruent.1D
│       ├── congruent_run1.txt
│       ├── congruent_run2.txt
│       ├── incongruent.1D
│       ├── incongruent_run1.txt
│       ├── incongruent_run2.txt
│       ├── sub-25_task-flanker_run-1_bold.nii.gz -> ../../.git/annex/objects/XW/1v/MD5E-s29473003--49b04e7e4b450ec5ef93ff02d4158775.nii.gz/MD5E-s29473003--49b04e7e4b450ec5ef93ff02d4158775.nii.gz
│       ├── sub-25_task-flanker_run-1_events.tsv
│       ├── sub-25_task-flanker_run-2_bold.nii.gz -> ../../.git/annex/objects/Qm/M7/MD5E-s29460132--b0e9039e9f33510631f229c8c2193285.nii.gz/MD5E-s29460132--b0e9039e9f33510631f229c8c2193285.nii.gz
│       └── sub-25_task-flanker_run-2_events.tsv
├── sub-26
│   ├── anat
│   │   └── sub-26_T1w.nii.gz -> ../../.git/annex/objects/kf/9F/MD5E-s10850250--5f103b2660f488e4afa193f9307c1291.nii.gz/MD5E-s10850250--5f103b2660f488e4afa193f9307c1291.nii.gz
│   └── func
│       ├── congruent.1D
│       ├── congruent_run1.txt
│       ├── congruent_run2.txt
│       ├── incongruent.1D
│       ├── incongruent_run1.txt
│       ├── incongruent_run2.txt
│       ├── sub-26_task-flanker_run-1_bold.nii.gz -> ../../.git/annex/objects/QV/10/MD5E-s30127491--8e30aa4bbfcc461bac8598bf621283c5.nii.gz/MD5E-s30127491--8e30aa4bbfcc461bac8598bf621283c5.nii.gz
│       ├── sub-26_task-flanker_run-1_events.tsv
│       ├── sub-26_task-flanker_run-2_bold.nii.gz -> ../../.git/annex/objects/3G/Q6/MD5E-s30162480--80fd132e7cb1600ab248249e78f6f1aa.nii.gz/MD5E-s30162480--80fd132e7cb1600ab248249e78f6f1aa.nii.gz
│       └── sub-26_task-flanker_run-2_events.tsv
├── subjList.txt
└── task-flanker_bold.json

81 directories, 350 files

Creating Timing Files

Condition-specific timing files are generated using the same approach described in the Preprocessing and GLM notebook. In brief:

• Onset times and durations are extracted from each subject’s events.tsv file.

• Trials are categorized into congruent and incongruent conditions.

• The make_Timings.sh script (from Andy’s AFNI_Scripts repository) is used to convert this event information into AFNI-compatible .1D timing files.

• For each subject, two timing files are created (one per condition), spanning both runs, and saved in the subject’s func/ directory.

These .1D timing files will then be used in the first-level GLM to model condition-specific brain responses.

![ -f ds000102/make_Timings.sh ] || wget -O ds000102/make_Timings.sh https://raw.githubusercontent.com/andrewjahn/AFNI_Scripts/master/make_Timings.sh

Running the Timing File Script

After placing the make_Timings.sh script into the ds000102/ directory, we can execute it from within the notebook:

!cd ds000102 && chmod +x make_Timings.sh && bash make_Timings.sh

/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \
/opt/afni-latest/afnipy/lib_afni1D.py:1302: SyntaxWarning: 'str' object is not callable; perhaps you missed a comma?
  print('** uncensor from vec: nt = %d, but nocen len = %d' \

! Note:

You may see a SyntaxWarning from AFNI's internal Python scripts when running this command — this can be safely ignored and does not affect the output.

Check the output:

!cat ds000102/sub-01/func/incongruent.1D

0 10 40 76 102 150 164 174 208 220 232 260 
0 54 64 76 88 130 144 154 196 246 274

2. Running Preprocessing and First-Level Analysis for All Subjects

All of the preprocessing and regression steps for subject sub-08 were introduced and explained in the example notebooks Preprocessing with AFNI and AFNI Preprocessing and GLM, both of which are highly inspired by Andy’s Brain Book’s tutorial.
These notebooks demonstrate how to use afni_proc.py to generate an automated pipeline and interpret each preprocessing and regression block.

Preprocessing and GLM Workflow:

➡️ setup ➡️ tcat ➡️ align ➡️ tlrc ➡️ volreg ➡️ blur ➡️ mask ➡️ scale ➡️ regress ➡️ 🧠

✅ Outputs: fitted time series, beta weights, and statistical maps from the GLM.

To replicate the preprocessing and GLM steps used for sub-08 across multiple participants, we loop over all 9 subjects (sub-01 to sub-09) and generate an individualized AFNI pipeline for each one using afni_proc.py. This automated approach performs several key operations:

• Loads each subject’s anatomical image and both functional runs.

• Specifies the full processing pipeline: alignment, linear registration to MNI space, motion correction, blurring, masking, scaling, and regression modeling.

• Models two stimulus conditions (congruent and incongruent) using a gamma basis function.

• Specifies two general linear tests (GLTs): incongruent - congruent and congruent - incongruent.

• Censors time points with excessive motion (> 0.3 mm), disables motion derivatives, and estimates spatial smoothness for later use in group analysis.

• Runs 3dREMLfit for improved model estimation and produces a Pythonic HTML review report for each subject.

To improve alignment robustness, the script is post-edited to insert the -init_xform AUTO_CENTER option into the @auto_tlrc command as this works better on this dataset.

Processing is executed in parallel using a process pool, with up to 3 subjects processed simultaneously. Each subject’s script is saved and executed in a controlled logging environment, which captures terminal output into a log file for transparency and troubleshooting.

This block ensures consistent preprocessing and first-level GLM estimation across all subjects in the dataset.

# Create directory for output
os.makedirs("afni_pro_glm", exist_ok=True)

# Main subject processing function
def process_subject(subj_id):
    subj = f"sub-{subj_id:02d}"
    anat = f"./ds000102/{subj}/anat/{subj}_T1w.nii.gz"
    func1 = f"./ds000102/{subj}/func/{subj}_task-flanker_run-1_bold.nii.gz"
    func2 = f"./ds000102/{subj}/func/{subj}_task-flanker_run-2_bold.nii.gz"
    stim1D_c = f"./ds000102/{subj}/func/congruent.1D"
    stim1D_i = f"./ds000102/{subj}/func/incongruent.1D"
    out_dir = f"./afni_pro_glm/{subj}.results"
    script_name = f"./afni_pro_glm/proc.{subj}.tcsh"
    log_file = f"./afni_pro_glm/output.{subj}.log"

    # Skip subject if already processed
    if os.path.exists(out_dir):
        return f"{subj} skipped (already processed)"

    cmd = [
        "afni_proc.py",
        "-subj_id", subj,
        "-script", script_name,
        "-scr_overwrite",
        "-out_dir", out_dir,
        "-blocks", "align", "tlrc", "volreg", "blur", "mask", "scale", "regress",
        "-copy_anat", anat,
        "-dsets", func1, func2,
        "-tcat_remove_first_trs", "0",
        "-align_opts_aea", "-giant_move",
        "-tlrc_base", "MNI_avg152T1+tlrc",
        "-volreg_align_to", "MIN_OUTLIER",
        "-volreg_align_e2a",
        "-volreg_tlrc_warp",
        "-blur_size", "4.0",
        "-regress_stim_times", stim1D_c, stim1D_i,
        "-regress_stim_labels", "congruent", "incongruent",
        "-regress_stim_types", "times", "times",
        "-regress_basis", "GAM",
        "-regress_opts_3dD",
        "-gltsym", "SYM: +incongruent -congruent", "-glt_label", "1", "incongruent-congruent",
        "-gltsym", "SYM: +congruent -incongruent", "-glt_label", "2", "congruent-incongruent",
        "-jobs", "8",                        #  speedup with multithreading
        "-GOFORIT", "0",                     #  safe default
        "-regress_no_motion_deriv",          #  disables motion derivatives (simpler model)
        "-regress_censor_motion", "0.3",     #  standard threshold
        "-regress_motion_per_run",           #  run-wise motion parameters
        "-regress_est_blur_epits",
        "-regress_est_blur_errts",
        "-regress_make_ideal_sum", "sum_ideal.1D",
        "-regress_reml_exec",                
        "-regress_run_clustsim", "no",       #  skip, since you'll do group-level stats separately
        "-html_review_style", "pythonic"
    ]

    try:
        # Step 1: Create the AFNI processing script
        subprocess.run(cmd, check=True)

        # Step 2: Insert -init_xform AUTO_CENTER into the @auto_tlrc command
        with open(script_name, 'r') as f:
            lines = f.readlines()
        for i, line in enumerate(lines):
            if line.strip().startswith("@auto_tlrc") and "AUTO_CENTER" not in line:
                lines[i] = line.strip() + " -init_xform AUTO_CENTER\n"
        with open(script_name, 'w') as f:
            f.writelines(lines)

        # Step 3: Run the AFNI tcsh script, logging output
        with open(log_file, "w") as logfile:
            proc = subprocess.Popen(
                ["tcsh", "-xef", script_name],
                stdout=subprocess.PIPE,
                stderr=subprocess.STDOUT,
                text=True
            )
            for line in proc.stdout:
                print(line, end="")     # Stream to console
                logfile.write(line)     # Log to file
            proc.wait()

        return f"{subj} {'done' if proc.returncode == 0 else 'failed'}"
        
    except subprocess.CalledProcessError as e:
        return f"{subj} failed: afni_proc.py error"
    except Exception as e:
        return f"{subj} failed: unexpected error\n{e}"

# ──────────────────────────────────────────────────────────────────────────────
# Main loop to process multiple subjects in parallel
if __name__ == "__main__":
    subject_ids = list(range(1, 10))  # sub-01 to sub-09
    results = []

    with ProcessPoolExecutor(max_workers=3) as executor:
        futures = {executor.submit(process_subject, sid): sid for sid in subject_ids}
        for future in tqdm(as_completed(futures), total=len(futures), desc="Subjects processed"):
            results.append(future.result())

    print("\nSummary of results:")
    for r in results:
        print(r)

Summary of results:
sub-01 skipped (already processed)
sub-03 skipped (already processed)
sub-02 skipped (already processed)
sub-04 skipped (already processed)
sub-05 skipped (already processed)
sub-06 skipped (already processed)
sub-07 skipped (already processed)
sub-08 skipped (already processed)
sub-09 skipped (already processed)

3. Group - Analysis

After estimating the first-level general linear model (GLM) for each subject, we will perform a group-level analysis to assess whether the Incongruent - Congruent contrast showed a consistent effect across subjects.

Creating a Group Mask

First, we’ll create a group-level mask by combining each subject’s individual mask using a logical union. This ensures that only voxels present in all subjects’ data are included in the group analysis:

! 3dmask_tool -input afni_pro_glm/sub-*.results/mask_group+tlrc.HEAD -prefix ./afni_pro_glm/group_mask+tlrc -union

++ processing 9 input dataset(s), NN=2...
++ padding all datasets by 0 (for dilations)
++ frac 0 over 9 volumes gives min count 0
++ voxel limits: 0 clipped, 73409 survived, 198224 were zero
++ writing result group_mask...
** ERROR: output dataset name 'group_mask' conflicts with existing file
** ERROR: dataset NOT written to disk!

3.1 Group-Level Analysis with 3dttest++

AFNI’s 3dttest++ performs a voxelwise one-sample t-test across subjects. This tests whether the average contrast estimate (e.g., Incongruent - Congruent) is significantly different from zero at each voxel.oxelwise t-scoresariability.

Identifying Contrast Sub-Brick

Before running the group-level test, we must determine which sub-brick contains the desired contrast. We use 3dinfo to inspect the subject-level stats+tlrc dataset and find the index of the contrast sub-brick corresponding to incongruent minus congruent (e.g., sub-brick #7, depending on how GLTs were defined in afni_proc.py):

! 3dinfo -verb ./afni_pro_glm/sub-08.results/stats.sub-08+tlrc.BRIK

++ 3dinfo: AFNI version=AFNI_21.2.00 (Jul  8 2021) [64-bit]

Dataset File:    stats.sub-08+tlrc
Identifier Code: XYZ_WJ-PX6plfBi-HLrMwwcEow  Creation Date: Tue Mar 10 07:16:43 2026
Template Space:  MNI
Dataset Type:    Func-Bucket (-fbuc)
Byte Order:      LSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode:    BRIK
Storage Space:   14,124,916 (14 million) bytes
Geometry String: "MATRIX(-3,0,0,90,0,-3,0,126,0,0,3,-72):61,73,61"
Data Axes Tilt:  Plumb
Data Axes Orientation:
  first  (x) = Left-to-Right
  second (y) = Posterior-to-Anterior
  third  (z) = Inferior-to-Superior   [-orient LPI]
R-to-L extent:   -90.000 [R] -to-    90.000 [L] -step-     3.000 mm [ 61 voxels]
A-to-P extent:   -90.000 [A] -to-   126.000 [P] -step-     3.000 mm [ 73 voxels]
I-to-S extent:   -72.000 [I] -to-   108.000 [S] -step-     3.000 mm [ 61 voxels]
Number of values stored at each pixel = 13
  -- At sub-brick #0 'Full_Fstat' datum type is float:            0 to       55.6688
     statcode = fift;  statpar = 2 268
  -- At sub-brick #1 'congruent#0_Coef' datum type is float:     -20.0682 to       19.7864
  -- At sub-brick #2 'congruent#0_Tstat' datum type is float:     -4.95626 to       7.66608
     statcode = fitt;  statpar = 268
  -- At sub-brick #3 'congruent_Fstat' datum type is float:            0 to       58.7687
     statcode = fift;  statpar = 1 268
  -- At sub-brick #4 'incongruent#0_Coef' datum type is float:     -16.9107 to       19.8846
  -- At sub-brick #5 'incongruent#0_Tstat' datum type is float:     -5.66548 to       9.71671
     statcode = fitt;  statpar = 268
  -- At sub-brick #6 'incongruent_Fstat' datum type is float:            0 to       94.4144
     statcode = fift;  statpar = 1 268
  -- At sub-brick #7 'incongruent-congruent_GLT#0_Coef' datum type is float:     -19.9548 to       21.7222
  -- At sub-brick #8 'incongruent-congruent_GLT#0_Tstat' datum type is float:     -4.39914 to       5.95293
     statcode = fitt;  statpar = 268
  -- At sub-brick #9 'incongruent-congruent_GLT_Fstat' datum type is float:            0 to       35.4373
     statcode = fift;  statpar = 1 268
  -- At sub-brick #10 'congruent-incongruent_GLT#0_Coef' datum type is float:     -21.7222 to       19.9548
  -- At sub-brick #11 'congruent-incongruent_GLT#0_Tstat' datum type is float:     -5.95293 to       4.39914
     statcode = fitt;  statpar = 268
  -- At sub-brick #12 'congruent-incongruent_GLT_Fstat' datum type is float:            0 to       35.4373
     statcode = fift;  statpar = 1 268

----- HISTORY -----
[jovyan@16f89e0677e8: Tue Mar 10 07:16:43 2026] {AFNI_21.2.00:linux_openmp_64} 3dDeconvolve -input pb03.sub-08.r01.scale+tlrc.HEAD pb03.sub-08.r02.scale+tlrc.HEAD -censor motion_sub-08_censor.1D -ortvec mot_demean.r01.1D mot_demean_r01 -ortvec mot_demean.r02.1D mot_demean_r02 -polort 2 -num_stimts 2 -stim_times 1 stimuli/congruent.1D GAM -stim_label 1 congruent -stim_times 2 stimuli/incongruent.1D GAM -stim_label 2 incongruent -gltsym 'SYM: +incongruent -congruent' -glt_label 1 incongruent-congruent -gltsym 'SYM: +congruent -incongruent' -glt_label 2 congruent-incongruent -jobs 8 -GOFORIT 0 -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.sub-08 -errts errts.sub-08 -bucket stats.sub-08
[jovyan@16f89e0677e8: Tue Mar 10 07:16:43 2026] Output prefix: stats.sub-08

This command lists all sub-bricks with their labels, allowing us to find the relevant contrast parameter estimate:

-- At sub-brick #7 'incongruent-congruent_GLT#0_Coef' datum type is float:     -19.9548 to       21.7222

Sub-bricks labeled with “Coef” represent contrast (beta) estimates, while “Tstat” or “Fstat” indicate test statistics. For group analysis, we will extract the Coef sub-brick (here: index [7]).

We then automate the 3dttest++ execution with the following steps:

- Set the base directory containing all subjects’ AFNI result folders. **

• Locate sub-brick [**7] for each subject (the contrast of interest).**

• Verify dat**aset existence to avoid processing missing subjects.

• Construct the 3dttest++ command with:

  • An output prefix for group results,

  • A group brain mask to constrain the analysis,

  • A label for the subject set (Inc-Con),

  • Subpaired with their corresponding contrast sub-brick pathssti**mates.

• Run **the command using subprocess.run() to capture and log output.

The resulting dataset (Flanker_Inc-Con_ttest+tlrc) contains:

• Effect size map: average contrast values across subjects

• T-statistic map: voxelwise t-values representing statistical significance

base_dir = os.path.abspath("./afni_pro_glm")

# Get all subject folders
subject_dirs = sorted(glob(os.path.join(base_dir, "sub-*.results")))

# Build paths to sub-brik 7 (e.g. Inc-Con contrast)
set_lines = []
for s in subject_dirs:
    sub_id = os.path.basename(s).replace('.results', '')
    stats_path = os.path.join(s, f"stats.{sub_id}+tlrc[7]")
    if os.path.exists(stats_path.replace('[7]', '.BRIK')) or os.path.exists(stats_path):  # extra check
        set_lines.append(f"{sub_id} {stats_path}")
    else:
        print(f"⚠️  Missing file for subject {sub_id}: {stats_path}")

# Build 3dttest++ command
cmd_list = [
    "3dttest++",
    "-prefix", os.path.join(base_dir, "group_results", "Flanker-Inc-Con_ttest"),
    "-mask", os.path.join(base_dir, "group_mask+tlrc"),
    "-setA", "Inc-Con"
]

# Add subject lines
for line in set_lines:
    cmd_list += line.split()

# Run the command
print("Running 3dttest++...")
print("\n")
print("Command:", " ".join(cmd_list))
result = subprocess.run(cmd_list, capture_output=True, text=True)

# Show output
print(result.stdout)
print(result.stderr)

Running 3dttest++...


Command: 3dttest++ -prefix /home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/group_results/Flanker-Inc-Con_ttest -mask /home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/group_mask+tlrc -setA Inc-Con sub-01 /home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/sub-01.results/stats.sub-01+tlrc[7] sub-02 /home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/sub-02.results/stats.sub-02+tlrc[7] sub-03 /home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/sub-03.results/stats.sub-03+tlrc[7] sub-04 /home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/sub-04.results/stats.sub-04+tlrc[7] sub-05 /home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/sub-05.results/stats.sub-05+tlrc[7] sub-06 /home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/sub-06.results/stats.sub-06+tlrc[7] sub-07 /home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/sub-07.results/stats.sub-07+tlrc[7] sub-08 /home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/sub-08.results/stats.sub-08+tlrc[7] sub-09 /home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/sub-09.results/stats.sub-09+tlrc[7]

++ 3dttest++: AFNI version=AFNI_21.2.00 (Jul  8 2021) [64-bit]
++ Authored by: Zhark++
++ 73409 voxels in -mask dataset
++ option -setA :: processing as LONG form (label label dset label dset ...)
++ have 9 volumes corresponding to option '-setA'
++ loading -setA datasets
++ t-testing:0123456789.0123456789.0123456789.0123456789.0123456789.!
++ ---------- End of analyses -- freeing workspaces ----------
++ Creating FDR curves in output dataset
*+ WARNING: Smallest FDR q [1 Inc-Con_Tstat] = 0.241757 ==> few true single voxel detections
 + Added 1 FDR curve to dataset
** ERROR: output dataset name 'Flanker-Inc-Con_ttest' conflicts with existing file
** ERROR: dataset NOT written to disk!
++ ----- 3dttest++ says so long, farewell, and happy trails to you :) -----

This code snippet automates running AFNI’s 3dttest++ for a group analysis of the Incongruent - Congruent contrast:

• Set the base directory where all subjects’ AFNI results are stored.

• Find all subject result folders matching the pattern sub-*.results.

• Build a list of dataset paths pointing to the 7th sub-brick [7] (the contrast of interest) in each subject’s stats dataset, verifying file existence and alerting if missing.

• Construct the 3dttest++ command with:

  • Output prefix for group results,

  • Group mask to restrict the test to voxels common across subjects,

  • Label for the group set (Inc-Con),

  • Subject IDs paired with their corresponding contrast sub-brick paths.

• Run the command as a subprocess, capturing and printing AFNI’s output and errors for review.

The resulting output (Flanker_Inc-Con_ttest+tlrc) contains:

• Effect size map: average contrast across subjects

• T-statistic map: voxelwise t-sores

3.2 Performing Group Analysis with 3dMEMA

To account for both the variability within subjects (parameter estimate differences) and the variability across subjects (contrast estimate precision), we will also perform a group-level analysis using AFNI’s 3dMEMA.

Unlike a simple t-test, 3dMEMA leverages each subject’s contrast estimate and corresponding t-statistic (or standard error), providing a more accurate mixed-effects model.

The steps we will take are:

• Build a set list containing each subject’s ID along with the paths to their contrast estimate (_REML+tlrc[7]) and t-statistic (_REML+tlrc[8]) sub-bricks.

• Verify that both files exist for each subject to avoid missing data errors.

• Construct the 3dMEMA command with an output prefix, the group mask, and the full subject set list.

• Run the command as a subprocess, capturing output for review.

This process will produce a group-level statistical map that balances effect size and reliability, offering a robust inference about the Incongruent - Congruent contrast across subjects.

# Build set list: all subjects in one set block
set_list = ["-set", "IncCon"]
for s in subject_dirs:
    sub_id = os.path.basename(s).replace(".results", "")
    coef_path = os.path.join(s, f"stats.{sub_id}_REML+tlrc[7]")
    tstat_path = os.path.join(s, f"stats.{sub_id}_REML+tlrc[8]")

    # Sanity check (optional)
    if os.path.exists(coef_path.replace("[7]", ".HEAD")) and os.path.exists(tstat_path.replace("[8]", ".HEAD")):
        set_list += [sub_id, coef_path, tstat_path]
    else:
        print(f"⚠️ Missing for {sub_id}:\n  {coef_path}\n  {tstat_path}")

# Full 3dMEMA command
cmd_list = [
    "3dMEMA",
    "-prefix", os.path.join(base_dir, "group_results", "Flanker_Inc-Con_MEMA"),
    "-mask", os.path.join(base_dir, "group_mask+tlrc"),
] + set_list

# Print and run
print("Running 3dMEMA...\n")
print("Command:", " ".join(cmd_list), "\n")
result = subprocess.run(cmd_list, capture_output=True, text=True)

print(result.stdout)
print(result.stderr)

Running 3dMEMA...

Command: 3dMEMA -prefix /home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/group_results/Flanker_Inc-Con_MEMA -mask /home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/group_mask+tlrc -set IncCon sub-01 /home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/sub-01.results/stats.sub-01_REML+tlrc[7] /home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/sub-01.results/stats.sub-01_REML+tlrc[8] sub-02 /home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/sub-02.results/stats.sub-02_REML+tlrc[7] /home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/sub-02.results/stats.sub-02_REML+tlrc[8] sub-03 /home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/sub-03.results/stats.sub-03_REML+tlrc[7] /home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/sub-03.results/stats.sub-03_REML+tlrc[8] sub-04 /home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/sub-04.results/stats.sub-04_REML+tlrc[7] /home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/sub-04.results/stats.sub-04_REML+tlrc[8] sub-05 /home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/sub-05.results/stats.sub-05_REML+tlrc[7] /home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/sub-05.results/stats.sub-05_REML+tlrc[8] sub-06 /home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/sub-06.results/stats.sub-06_REML+tlrc[7] /home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/sub-06.results/stats.sub-06_REML+tlrc[8] sub-07 /home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/sub-07.results/stats.sub-07_REML+tlrc[7] /home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/sub-07.results/stats.sub-07_REML+tlrc[8] sub-08 /home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/sub-08.results/stats.sub-08_REML+tlrc[7] /home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/sub-08.results/stats.sub-08_REML+tlrc[8] sub-09 /home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/sub-09.results/stats.sub-09_REML+tlrc[7] /home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/sub-09.results/stats.sub-09_REML+tlrc[8]


** Error: 
   File /home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/group_results/Flanker_Inc-Con_MEMAexists! Try a different name.

3.3 Visualizing Group-Level Results

Now that we have completed both group analyses — one with 3dttest++ and one with 3dMEMA — let’s visualize the resulting voxelwise t-statistic maps.

Steps:

1. Convert AFNI datasets to NIfTI format using 3dcopy, to ensure compatibility with Python neuroimaging tools like nilearn.

2. Extract the t-statistic sub-brick (sub-brick index [1]) using 3dTcat. This gives us:

   • Inc-Con_Tstat from the 3dttest++ result

   • IncCon_Tstat from the 3dMEMA result

3. Load the statistical maps into Python using nilearn.image.load_img().

4. Apply voxelwise thresholding:

   • A two-tailed threshold of T > 3.3

   • A minimum cluster size of 40 contiguous voxels

   This reduces noise and highlights clusters likely to reflect meaningful effects.

Note on Multiple Comparison Correction:
Cluster-size correction using 3dClustSim requires stable estimates of spatial smoothness, which generally requires at least 14 subjects.
Since our analysis includes only 9 subjects, we do not apply 3dClustSim or other parametric corrections.
Instead, we apply an uncorrected voxelwise threshold (T > 3.3) with a minimum cluster size of 40 voxels.
This approach is intended for exploratory visualization only and should not be used for formal statistical inference.

5. Plot the thresholded maps using nilearn.plotting.plot_stat_map() to qualitatively compare the spatial activation patterns between the two group-level methods.

This approach allows us to visually inspect and compare the sensitivity and spatial extent of effects revealed by the simple one-sample t-test (3dttest++) and the mixed-effects model (3dMEMA) for the Incongruent - Congruent contrast.

! 3dcopy ./afni_pro_glm/group_results/Flanker-Inc-Con_ttest+tlrc ./afni_pro_glm/group_results/Flanker-Inc-Con_ttest.nii.gz
! 3dcopy ./afni_pro_glm/group_results/Flanker_Inc-Con_MEMA+tlrc ./afni_pro_glm/group_results/Flanker_Inc-Con_MEMA.nii.gz

++ 3dcopy: AFNI version=AFNI_21.2.00 (Jul  8 2021) [64-bit]
** ERROR: output dataset name 'Flanker-Inc-Con_ttest.nii.gz' conflicts with existing file
** ERROR: dataset NOT written to disk!
++ 3dcopy: AFNI version=AFNI_21.2.00 (Jul  8 2021) [64-bit]
** ERROR: output dataset name 'Flanker_Inc-Con_MEMA.nii.gz' conflicts with existing file
** ERROR: dataset NOT written to disk!

! 3dinfo -verb ./afni_pro_glm/group_results/Flanker-Inc-Con_ttest.nii.gz

++ 3dinfo: AFNI version=AFNI_21.2.00 (Jul  8 2021) [64-bit]

Dataset File:    /home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/group_results/Flanker-Inc-Con_ttest.nii.gz
Identifier Code: XYZ_SARl6aENuvTXlHZENBwAYA  Creation Date: Tue Mar 10 07:22:08 2026
Template Space:  MNI
Dataset Type:    Anat Bucket (-abuc)
Byte Order:      LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode:    NIFTI
Storage Space:   2,173,064 (2.2 million) bytes
Geometry String: "MATRIX(-3,0,0,90,0,-3,0,126,0,0,3,-72):61,73,61"
Data Axes Tilt:  Plumb
Data Axes Orientation:
  first  (x) = Left-to-Right
  second (y) = Posterior-to-Anterior
  third  (z) = Inferior-to-Superior   [-orient LPI]
R-to-L extent:   -90.000 [R] -to-    90.000 [L] -step-     3.000 mm [ 61 voxels]
A-to-P extent:   -90.000 [A] -to-   126.000 [P] -step-     3.000 mm [ 73 voxels]
I-to-S extent:   -72.000 [I] -to-   108.000 [S] -step-     3.000 mm [ 61 voxels]
Number of values stored at each pixel = 2
  -- At sub-brick #0 'Inc-Con_mean' datum type is float:     -2.86885 to       2.65067
  -- At sub-brick #1 'Inc-Con_Tstat' datum type is float:     -7.60381 to       9.81179
     statcode = fitt;  statpar = 8

----- HISTORY -----
[jovyan@16f89e0677e8: Tue Mar 10 07:21:01 2026] {AFNI_21.2.00:linux_openmp_64} 3dttest++ -prefix /home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/group_results/Flanker-Inc-Con_ttest -mask /home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/group_mask+tlrc -setA Inc-Con sub-01 '/home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/sub-01.results/stats.sub-01+tlrc[7]' sub-02 '/home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/sub-02.results/stats.sub-02+tlrc[7]' sub-03 '/home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/sub-03.results/stats.sub-03+tlrc[7]' sub-04 '/home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/sub-04.results/stats.sub-04+tlrc[7]' sub-05 '/home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/sub-05.results/stats.sub-05+tlrc[7]' sub-06 '/home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/sub-06.results/stats.sub-06+tlrc[7]' sub-07 '/home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/sub-07.results/stats.sub-07+tlrc[7]' sub-08 '/home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/sub-08.results/stats.sub-08+tlrc[7]' sub-09 '/home/jovyan/workspace/books/examples/functional_imaging/afni_pro_glm/sub-09.results/stats.sub-09+tlrc[7]'
[jovyan@16f89e0677e8: Tue Mar 10 07:22:08 2026] {AFNI_21.2.00:linux_openmp_64} 3dcopy ./afni_pro_glm/group_results/Flanker-Inc-Con_ttest+tlrc ./afni_pro_glm/group_results/Flanker-Inc-Con_ttest.nii.gz

# Copy sub-brik 1 (T-statistic) for ttest++
!3dTcat -prefix ./afni_pro_glm/group_results/Flanker-Inc-Con_ttest_Tstat.nii.gz './afni_pro_glm/group_results/Flanker-Inc-Con_ttest+tlrc[1]'

# Copy sub-brik 1 (T-statistic) for MEMA
!3dTcat -prefix ./afni_pro_glm/group_results/Flanker_Inc-Con_MEMA_Tstat.nii.gz './afni_pro_glm/group_results/Flanker_Inc-Con_MEMA+tlrc[1]'

++ 3dTcat: AFNI version=AFNI_21.2.00 (Jul  8 2021) [64-bit]
** ERROR: output dataset name 'Flanker-Inc-Con_ttest_Tstat.nii.gz' conflicts with existing file
** ERROR: dataset NOT written to disk!
++ elapsed time = 0.1 s
++ 3dTcat: AFNI version=AFNI_21.2.00 (Jul  8 2021) [64-bit]
** ERROR: output dataset name 'Flanker_Inc-Con_MEMA_Tstat.nii.gz' conflicts with existing file
** ERROR: dataset NOT written to disk!
++ elapsed time = 0.1 s

# Load T-stat map (3dttest++ and 3dMEMA results)
img_ttest = image.load_img("./afni_pro_glm/group_results/Flanker-Inc-Con_ttest_Tstat.nii.gz")
img_mema = image.load_img("./afni_pro_glm/group_results/Flanker_Inc-Con_MEMA_Tstat.nii.gz")


threshold = 3.3 

# Apply uncorrected voxel threshold (T > 3.3 ≈ p < 0.001)
# and minimum cluster size of 40 voxels
thresholded_img_ttest = image.threshold_img(
    img_ttest,
    threshold=threshold,
    cluster_threshold=40,
    two_sided=True,  
    copy_header=True
    
)

thresholded_img_mema = image.threshold_img(
    img_mema,
    threshold=threshold,
    cluster_threshold=40,
    two_sided=True,
    copy_header=True
    
)

# Plot result
plotting.plot_stat_map(
    thresholded_img_ttest,
    title="3dttest++ (p<0.001, k≥40 vox)",
    threshold=threshold,
    colorbar=True
)

plotting.plot_stat_map(
    thresholded_img_mema,
    title="3dMEMA (p<0.001, k≥40 vox)",
    threshold=threshold,
    colorbar=True
)
plotting.show()

4. ROI Analysis

4.1 ROI Analysis: Atlas-Based MidACC Mask

To investigate group-level effects within a specific anatomical region, we use an atlas-based Region of Interest (ROI) mask focusing on the mid anterior cingulate cortex (midACC).

1. Identify Available Atlases:

We begin by confirming the available atlases using:

!whereami -show_atlas_code

This lists all atlases bundled with AFNI.

! whereami -show_atlas_code

++ Input coordinates orientation set by default rules to RAI

Atlas MNI_Glasser_HCP_v1.0,      360 regions
----------- Begin regions for MNI_Glasser_HCP_v1.0 atlas-----------
u:L_Primary_Visual_Cortex:1  
u:R_Primary_Visual_Cortex:1001
u:L_Medial_Superior_Temporal_Area:2  
u:R_Medial_Superior_Temporal_Area:1002
u:L_Sixth_Visual_Area:3  
u:R_Sixth_Visual_Area:1003
u:L_Second_Visual_Area:4  
u:R_Second_Visual_Area:1004
u:L_Third_Visual_Area:5  
u:R_Third_Visual_Area:1005
u:L_Fourth_Visual_Area:6  
u:R_Fourth_Visual_Area:1006
u:L_Eighth_Visual_Area:7  
u:R_Eighth_Visual_Area:1007
u:L_Primary_Motor_Cortex:8  
u:R_Primary_Motor_Cortex:1008
u:L_Primary_Sensory_Cortex:9  
u:R_Primary_Sensory_Cortex:1009
u:L_Frontal_Eye_Fields:10 
u:R_Frontal_Eye_Fields:1010
u:L_Premotor_Eye_Fields:11 
u:R_Premotor_Eye_Fields:1011
u:L_Area_55b:12 
u:R_Area_55b:1012
u:L_Area_V3A:13 
u:R_Area_V3A:1013
u:L_RetroSplenial_Complex:14 
u:R_RetroSplenial_Complex:1014
u:L_Parieto-Occipital_Sulcus_Area_2:15 
u:R_Parieto-Occipital_Sulcus_Area_2:1015
u:L_Seventh_Visual_Area:16 
u:R_Seventh_Visual_Area:1016
u:L_IntraParietal_Sulcus_Area_1:17 
u:R_IntraParietal_Sulcus_Area_1:1017
u:L_Fusiform_Face_Complex:18 
u:R_Fusiform_Face_Complex:1018
u:L_Area_V3B:19 
u:R_Area_V3B:1019
u:L_Area_Lateral_Occipital_1:20 
u:R_Area_Lateral_Occipital_1:1020
u:L_Area_Lateral_Occipital_2:21 
u:R_Area_Lateral_Occipital_2:1021
u:L_Posterior_InferoTemporal:22 
u:R_Posterior_InferoTemporal:1022
u:L_Middle_Temporal_Area:23 
u:R_Middle_Temporal_Area:1023
u:L_Primary_Auditory_Cortex:24 
u:R_Primary_Auditory_Cortex:1024
u:L_PeriSylvian_Language_Area:25 
u:R_PeriSylvian_Language_Area:1025
u:L_Superior_Frontal_Language_Area:26 
u:R_Superior_Frontal_Language_Area:1026
u:L_PreCuneus_Visual_Area:27 
u:R_PreCuneus_Visual_Area:1027
u:L_Superior_Temporal_Visual_Area:28 
u:R_Superior_Temporal_Visual_Area:1028
u:L_Medial_Area_7P:29 
u:R_Medial_Area_7P:1029
u:L_Area_7m:30 
u:R_Area_7m:1030
u:L_Parieto-Occipital_Sulcus_Area_1:31 
u:R_Parieto-Occipital_Sulcus_Area_1:1031
u:L_Area_23d:32 
u:R_Area_23d:1032
u:L_Area_ventral_23_a+b:33 
u:R_Area_ventral_23_a+b:1033
u:L_Area_dorsal_23_a+b:34 
u:R_Area_dorsal_23_a+b:1034
u:L_Area_31p_ventral:35 
u:R_Area_31p_ventral:1035
u:L_Area_5m:36 
u:R_Area_5m:1036
u:L_Area_5m_ventral:37 
u:R_Area_5m_ventral:1037
u:L_Area_23c:38 
u:R_Area_23c:1038
u:L_Area_5L:39 
u:R_Area_5L:1039
u:L_Dorsal_Area_24d:40 
u:R_Dorsal_Area_24d:1040
u:L_Ventral_Area_24d:41 
u:R_Ventral_Area_24d:1041
u:L_Lateral_Area_7A:42 
u:R_Lateral_Area_7A:1042
u:L_Supplementary_And_Cingulate_Eye:43 
u:R_Supplementary_And_Cingulate_Eye:1043
u:L_Area_6m_anterior:44 
u:R_Area_6m_anterior:1044
u:L_Medial_Area_7A:45 
u:R_Medial_Area_7A:1045
u:L_Lateral_Area_7P:46 
u:R_Lateral_Area_7P:1046
u:L_Area_7PC:47 
u:R_Area_7PC:1047
u:L_Area_Lateral_IntraParietal_ventral:48 
u:R_Area_Lateral_IntraParietal_ventral:1048
u:L_Ventral_IntraParietal_Complex:49 
u:R_Ventral_IntraParietal_Complex:1049
u:L_Medial_IntraParietal_Area:50 
u:R_Medial_IntraParietal_Area:1050
u:L_Area_1:51 
u:R_Area_1:1051
u:L_Area_2:52 
u:R_Area_2:1052
u:L_Area_3a:53 
u:R_Area_3a:1053
u:L_Dorsal_area_6:54 
u:R_Dorsal_area_6:1054
u:L_Area_6mp:55 
u:R_Area_6mp:1055
u:L_Ventral_Area_6:56 
u:R_Ventral_Area_6:1056
u:L_Area_Posterior_24_prime:57 
u:R_Area_Posterior_24_prime:1057
u:L_Area_33_prime:58 
u:R_Area_33_prime:1058
u:L_Anterior_24_prime:59 
u:R_Anterior_24_prime:1059
u:L_Area_p32_prime:60 
u:R_Area_p32_prime:1060
u:L_Area_a24:61 
u:R_Area_a24:1061
u:L_Area_dorsal_32:62 
u:R_Area_dorsal_32:1062
u:L_Area_8BM:63 
u:R_Area_8BM:1063
u:L_Area_p32:64 
u:R_Area_p32:1064
u:L_Area_10r:65 
u:R_Area_10r:1065
u:L_Area_47m:66 
u:R_Area_47m:1066
u:L_Area_8Av:67 
u:R_Area_8Av:1067
u:L_Area_8Ad:68 
u:R_Area_8Ad:1068
u:L_Area_9_Middle:69 
u:R_Area_9_Middle:1069
u:L_Area_8B_Lateral:70 
u:R_Area_8B_Lateral:1070
u:L_Area_9_Posterior:71 
u:R_Area_9_Posterior:1071
u:L_Area_10d:72 
u:R_Area_10d:1072
u:L_Area_8C:73 
u:R_Area_8C:1073
u:L_Area_44:74 
u:R_Area_44:1074
u:L_Area_45:75 
u:R_Area_45:1075
u:L_Area_47l_(47_lateral):76 
u:R_Area_47l_(47_lateral):1076
u:L_Area_anterior_47r:77 
u:R_Area_anterior_47r:1077
u:L_Rostral_Area_6:78 
u:R_Rostral_Area_6:1078
u:L_Area_IFJa:79 
u:R_Area_IFJa:1079
u:L_Area_IFJp:80 
u:R_Area_IFJp:1080
u:L_Area_IFSp:81 
u:R_Area_IFSp:1081
u:L_Area__IFSa:82 
u:R_Area__IFSa:1082
u:L_Area_posterior_9-46v:83 
u:R_Area_posterior_9-46v:1083
u:L_Area_46:84 
u:R_Area_46:1084
u:L_Area_anterior_9-46v:85 
u:R_Area_anterior_9-46v:1085
u:L_Area_9-46d:86 
u:R_Area_9-46d:1086
u:L_Area_9_anterior:87 
u:R_Area_9_anterior:1087
u:L_Area_10v:88 
u:R_Area_10v:1088
u:L_Area_anterior_10p:89 
u:R_Area_anterior_10p:1089
u:L_Polar_10p:90 
u:R_Polar_10p:1090
u:L_Area_11l:91 
u:R_Area_11l:1091
u:L_Area_13l:92 
u:R_Area_13l:1092
u:L_Orbital_Frontal_Complex:93 
u:R_Orbital_Frontal_Complex:1093
u:L_Area_47s:94 
u:R_Area_47s:1094
u:L_Area_Lateral_IntraParietal_dorsal:95 
u:R_Area_Lateral_IntraParietal_dorsal:1095
u:L_Area_6_anterior:96 
u:R_Area_6_anterior:1096
u:L_Inferior_6-8_Transitional_Area:97 
u:R_Inferior_6-8_Transitional_Area:1097
u:L_Superior_6-8_Transitional_Area:98 
u:R_Superior_6-8_Transitional_Area:1098
u:L_Area_43:99 
u:R_Area_43:1099
u:L_Area_OP4/PV:100
u:R_Area_OP4/PV:1100
u:L_Area_OP1/SII:101
u:R_Area_OP1/SII:1101
u:L_Area_OP2-3/VS:102
u:R_Area_OP2-3/VS:1102
u:L_Area_52:103
u:R_Area_52:1103
u:L_RetroInsular_Cortex:104
u:R_RetroInsular_Cortex:1104
u:L_Area_PFcm:105
u:R_Area_PFcm:1105
u:L_Posterior_Insular_Area_2:106
u:R_Posterior_Insular_Area_2:1106
u:L_Area_TA2:107
u:R_Area_TA2:1107
u:L_Frontal_Opercular_Area_4:108
u:R_Frontal_Opercular_Area_4:1108
u:L_Middle_Insular_Area:109
u:R_Middle_Insular_Area:1109
u:L_Piriform_Cortex:110
u:R_Piriform_Cortex:1110
u:L_Anterior_Ventral_Insular_Area:111
u:R_Anterior_Ventral_Insular_Area:1111
u:L_Anterior_Agranular_Insula_Complex:112
u:R_Anterior_Agranular_Insula_Complex:1112
u:L_Frontal_Opercular_Area_1:113
u:R_Frontal_Opercular_Area_1:1113
u:L_Frontal_Opercular_Area_3:114
u:R_Frontal_Opercular_Area_3:1114
u:L_Frontal_Opercular_Area_2:115
u:R_Frontal_Opercular_Area_2:1115
u:L_Area_PFt:116
u:R_Area_PFt:1116
u:L_Anterior_IntraParietal_Area:117
u:R_Anterior_IntraParietal_Area:1117
u:L_Entorhinal_Cortex:118
u:R_Entorhinal_Cortex:1118
u:L_PreSubiculum:119
u:R_PreSubiculum:1119
u:L_Hippocampus:120
u:R_Hippocampus:1120
u:L_ProStriate_Area:121
u:R_ProStriate_Area:1121
u:L_Perirhinal_Ectorhinal_Cortex:122
u:R_Perirhinal_Ectorhinal_Cortex:1122
u:L_Area_STGa:123
u:R_Area_STGa:1123
u:L_ParaBelt_Complex:124
u:R_ParaBelt_Complex:1124
u:L_Auditory_5_Complex:125
u:R_Auditory_5_Complex:1125
u:L_ParaHippocampal_Area_1:126
u:R_ParaHippocampal_Area_1:1126
u:L_ParaHippocampal_Area_3:127
u:R_ParaHippocampal_Area_3:1127
u:L_Area_STSd_anterior:128
u:R_Area_STSd_anterior:1128
u:L_Area_STSd_posterior:129
u:R_Area_STSd_posterior:1129
u:L_Area_STSv_posterior:130
u:R_Area_STSv_posterior:1130
u:L_Area_TG_dorsal:131
u:R_Area_TG_dorsal:1131
u:L_Area_TE1_anterior:132
u:R_Area_TE1_anterior:1132
u:L_Area_TE1_posterior:133
u:R_Area_TE1_posterior:1133
u:L_Area_TE2_anterior:134
u:R_Area_TE2_anterior:1134
u:L_Area_TF:135
u:R_Area_TF:1135
u:L_Area_TE2_posterior:136
u:R_Area_TE2_posterior:1136
u:L_Area_PHT:137
u:R_Area_PHT:1137
u:L_Area_PH:138
u:R_Area_PH:1138
u:L_Area_TemporoParietoOccipital_Junction_1:139
u:R_Area_TemporoParietoOccipital_Junction_1:1139
u:L_Area_TemporoParietoOccipital_Junction_2:140
u:R_Area_TemporoParietoOccipital_Junction_2:1140
u:L_Area_TemporoParietoOccipital_Junction_3:141
u:R_Area_TemporoParietoOccipital_Junction_3:1141
u:L_Dorsal_Transitional_Visual_Area:142
u:R_Dorsal_Transitional_Visual_Area:1142
u:L_Area_PGp:143
u:R_Area_PGp:1143
u:L_Area_IntraParietal_2:144
u:R_Area_IntraParietal_2:1144
u:L_Area_IntraParietal_1:145
u:R_Area_IntraParietal_1:1145
u:L_Area_IntraParietal_0:146
u:R_Area_IntraParietal_0:1146
u:L_Area_PF_opercular:147
u:R_Area_PF_opercular:1147
u:L_Area_PF_Complex:148
u:R_Area_PF_Complex:1148
u:L_Area_PFm_Complex:149
u:R_Area_PFm_Complex:1149
u:L_Area_PGi:150
u:R_Area_PGi:1150
u:L_Area_PGs:151
u:R_Area_PGs:1151
u:L_Area_V6A:152
u:R_Area_V6A:1152
u:L_VentroMedial_Visual_Area_1:153
u:R_VentroMedial_Visual_Area_1:1153
u:L_VentroMedial_Visual_Area_3:154
u:R_VentroMedial_Visual_Area_3:1154
u:L_ParaHippocampal_Area_2:155
u:R_ParaHippocampal_Area_2:1155
u:L_Area_V4t:156
u:R_Area_V4t:1156
u:L_Area_FST:157
u:R_Area_FST:1157
u:L_Area_V3CD:158
u:R_Area_V3CD:1158
u:L_Area_Lateral_Occipital_3:159
u:R_Area_Lateral_Occipital_3:1159
u:L_VentroMedial_Visual_Area_2:160
u:R_VentroMedial_Visual_Area_2:1160
u:L_Area_31pd:161
u:R_Area_31pd:1161
u:L_Area_31a:162
u:R_Area_31a:1162
u:L_Ventral_Visual_Complex:163
u:R_Ventral_Visual_Complex:1163
u:L_Area_25:164
u:R_Area_25:1164
u:L_Area_s32:165
u:R_Area_s32:1165
u:L_posterior_OFC_Complex:166
u:R_posterior_OFC_Complex:1166
u:L_Area_Posterior_Insular_1:167
u:R_Area_Posterior_Insular_1:1167
u:L_Insular_Granular_Complex:168
u:R_Insular_Granular_Complex:1168
u:L_Area_Frontal_Opercular:169
u:R_Area_Frontal_Opercular:1169
u:L_Area_posterior_10p:170
u:R_Area_posterior_10p:1170
u:L_Area_posterior_47r:171
u:R_Area_posterior_47r:1171
u:L_Area_TG_Ventral:172
u:R_Area_TG_Ventral:1172
u:L_Medial_Belt_Complex:173
u:R_Medial_Belt_Complex:1173
u:L_Lateral_Belt_Complex:174
u:R_Lateral_Belt_Complex:1174
u:L_Auditory_4_Complex:175
u:R_Auditory_4_Complex:1175
u:L_Area_STSv_anterior:176
u:R_Area_STSv_anterior:1176
u:L_Area_TE1_Middle:177
u:R_Area_TE1_Middle:1177
u:L_Para-Insular_Area:178
u:R_Para-Insular_Area:1178
u:L_Area_anterior_32_prime:179
u:R_Area_anterior_32_prime:1179
u:L_Area_posterior_24:180
u:R_Area_posterior_24:1180
----------- End regions for MNI_Glasser_HCP_v1.0 atlas --------------

Atlas Brainnetome_1.0,      246 regions
----------- Begin regions for Brainnetome_1.0 atlas-----------
u:A8m_left:1  
u:A8dl_left:3  
u:A9l_left:5  
u:A6dl_left:7  
u:A6m_left:9  
u:A9m_left:11 
u:A10m_left:13 
u:A9/46d_left:15 
u:IFJ_left:17 
u:A46_left:19 
u:A9/46v_left:21 
u:A8vl_left:23 
u:A6vl_left:25 
u:A10l_left:27 
u:A44d_left:29 
u:IFS_left:31 
u:A45c_left:33 
u:A45r_left:35 
u:A44op_left:37 
u:A44v_left:39 
u:A14m_left:41 
u:A12/47o_left:43 
u:A11l_left:45 
u:A11m_left:47 
u:A13_left:49 
u:A12/47l_left:51 
u:A4hf_left:53 
u:A6cdl_left:55 
u:A4ul_left:57 
u:A4t_left:59 
u:A4tl_left:61 
u:A6cvl_left:63 
u:A1/2/3ll_left:65 
u:A4ll_left:67 
u:A38m_left:69 
u:A41/42_left:71 
u:TE1.0_1.2_left:73 
u:A22c_left:75 
u:A38l_left:77 
u:A22r_left:79 
u:A21c_left:81 
u:A21r_left:83 
u:A37dl_left:85 
u:aSTS_left:87 
u:A20iv_left:89 
u:A37elv_left:91 
u:A20r_left:93 
u:A20il_left:95 
u:A37vl_left:97 
u:A20cl_left:99 
u:A20cv_left:101
u:A20rv_left:103
u:A37mv_left:105
u:A37lv_left:107
u:A35/36r_left:109
u:A35/36c_left:111
u:TL_left:113
u:A28/34_left:115
u:TI_left:117
u:TH_left:119
u:rpSTS_left:121
u:cpSTS_left:123
u:A7r_left:125
u:A7c_left:127
u:A5l_left:129
u:A7pc_left:131
u:A7ip_left:133
u:A39c_left:135
u:A39rd_left:137
u:A40rd_left:139
u:A40c_left:141
u:A39rv_left:143
u:A40rv_left:145
u:A7m_left:147
u:A5m_left:149
u:dmPOS_left:151
u:A31_left:153
u:A1/2/3ulhf_left:155
u:A1/2/3tonIa_left:157
u:A2_left:159
u:A1/2/3tru_left:161
u:G_left:163
u:vIa_left:165
u:dIa_left:167
u:vId/vIg_left:169
u:dIg_left:171
u:dId_left:173
u:A23d_left:175
u:A24rv_left:177
u:A32p_left:179
u:A23v_left:181
u:A24cd_left:183
u:A23c_left:185
u:A32sg_left:187
u:cLinG_left:189
u:rCunG_left:191
u:cCunG_left:193
u:rLinG_left:195
u:vmPOS_left:197
u:mOccG_left:199
u:V5/MT+_left:201
u:OPC_left:203
u:iOccG_left:205
u:msOccG_left:207
u:lsOccG_left:209
u:mAmyg_left:211
u:lAmyg_left:213
u:rHipp_left:215
u:cHipp_left:217
u:vCa_left:219
u:GP_left:221
u:NAC_left:223
u:vmPu_left:225
u:dCa_left:227
u:dlPu_left:229
u:mPFtha_left:231
u:mPMtha_left:233
u:Stha_left:235
u:rTtha_left:237
u:PPtha_left:239
u:Otha_left:241
u:cTtha_left:243
u:lPFtha_left:245
u:A8m_right:2  
u:A8dl_right:4  
u:A9l_right:6  
u:A6dl_right:8  
u:A6m_right:10 
u:A9m_right:12 
u:A10m_right:14 
u:A9/46d_right:16 
u:IFJ_right:18 
u:A46_right:20 
u:A9/46v_right:22 
u:A8vl_right:24 
u:A6vl_right:26 
u:A10l_right:28 
u:A44d_right:30 
u:IFS_right:32 
u:A45c_right:34 
u:A45r_right:36 
u:A44op_right:38 
u:A44v_right:40 
u:A14m_right:42 
u:A12/47o_right:44 
u:A11l_right:46 
u:A11m_right:48 
u:A13_right:50 
u:A12/47l_right:52 
u:A4hf_right:54 
u:A6cdl_right:56 
u:A4ul_right:58 
u:A4t_right:60 
u:A4tl_right:62 
u:A6cvl_right:64 
u:A1/2/3ll_right:66 
u:A4ll_right:68 
u:A38m_right:70 
u:A41/42_right:72 
u:TE1.0_1.2_right:74 
u:A22c_right:76 
u:A38l_right:78 
u:A22r_right:80 
u:A21c_right:82 
u:A21r_right:84 
u:A37dl_right:86 
u:aSTS_right:88 
u:A20iv_right:90 
u:A37elv_right:92 
u:A20r_right:94 
u:A20il_right:96 
u:A37vl_right:98 
u:A20cl_right:100
u:A20cv_right:102
u:A20rv_right:104
u:A37mv_right:106
u:A37lv_right:108
u:A35/36r_right:110
u:A35/36c_right:112
u:TL_right:114
u:A28/34_right:116
u:TI_right:118
u:TH_right:120
u:rpSTS_right:122
u:cpSTS_right:124
u:A7r_right:126
u:A7c_right:128
u:A5l_right:130
u:A7pc_right:132
u:A7ip_right:134
u:A39c_right:136
u:A39rd_right:138
u:A40rd_right:140
u:A40c_right:142
u:A39rv_right:144
u:A40rv_right:146
u:A7m_right:148
u:A5m_right:150
u:dmPOS_right:152
u:A31_right:154
u:A1/2/3ulhf_right:156
u:A1/2/3tonIa_right:158
u:A2_right:160
u:A1/2/3tru_right:162
u:G_right:164
u:vIa_right:166
u:dIa_right:168
u:vId/vIg_right:170
u:dIg_right:172
u:dId_right:174
u:A23d_right:176
u:A24rv_right:178
u:A32p_right:180
u:A23v_right:182
u:A24cd_right:184
u:A23c_right:186
u:A32sg_right:188
u:cLinG_right:190
u:rCunG_right:192
u:cCunG_right:194
u:rLinG_right:196
u:vmPOS_right:198
u:mOccG_right:200
u:V5/MT+_right:202
u:OPC_right:204
u:iOccG_right:206
u:msOccG_right:208
u:lsOccG_right:210
u:mAmyg_right:212
u:lAmyg_right:214
u:rHipp_right:216
u:cHipp_right:218
u:vCa_right:220
u:GP_right:222
u:NAC_right:224
u:vmPu_right:226
u:dCa_right:228
u:dlPu_right:230
u:mPFtha_right:232
u:mPMtha_right:234
u:Stha_right:236
u:rTtha_right:238
u:PPtha_right:240
u:Otha_right:242
u:cTtha_right:244
u:lPFtha_right:246
----------- End regions for Brainnetome_1.0 atlas --------------

Atlas CA_MPM_22_MNI,      100 regions
----------- Begin regions for CA_MPM_22_MNI atlas-----------
u:Interposed_Nucleus:111
u:Amygdala_(AStr):193
u:Amygdala_(CM):133
u:Amygdala_(LB):202
u:Amygdala_(SF):151
u:Area_FG3:117
u:Area_1:106
u:Area_2:243
u:Area_25:178
u:Area_33:119
u:Area_3a:250
u:Area_3b:187
u:Area_44:246
u:Area_45:129
u:Area_4a:160
u:Area_4p:191
u:Area_5Ci_(SPL):185
u:Area_5L_(SPL):159
u:Area_5M_(SPL):241
u:Area_7A_(SPL):165
u:Area_7M_(SPL):120
u:Area_7P_(SPL):224
u:Area_7PC_(SPL):167
u:Area_FG1:148
u:Area_FG2:171
u:Area_FG4:123
u:Area_Fo1:170
u:Area_Fo2:109
u:Area_Fo3:145
u:Area_Fp1:219
u:Area_Fp2:230
u:Area_Id1:126
u:Area_Ig1:236
u:Area_Ig2:204
u:Area_OP1_(SII):122
u:Area_OP2_(PIVC):139
u:Area_OP3_(VS):147
u:Area_OP4_(PV):173
u:Area_PF_(IPL):136
u:Area_PFcm_(IPL):153
u:Area_PFm_(IPL):128
u:Area_PFop_(IPL):125
u:Area_PFt_(IPL):240
u:Area_PGa_(IPL):201
u:Area_PGp_(IPL):198
u:Area_TE_1.0:210
u:Area_TE_1.1:213
u:Area_TE_1.2:218
u:Area_TE_3:181
u:Area_hIP1_(IPS):131
u:Area_hIP2_(IPS):226
u:Area_hIP3_(IPS):157
u:Area_hOc1_(V1):249
u:Area_hOc2_(V2):252
u:Area_hOc3d_(V3d):199
u:Area_hOc3v_(V3v):108
u:Area_hOc4d_(V3A):143
u:Area_hOc4la:162
u:Area_hOc4lp:233
u:Area_hOc4v_(V4(v)):103
u:Area_hOc5_(V5/MT):105
u:Area_s24:253
u:Area_s32:102
u:BF_(Ch_1-3):114
u:BF_(Ch_4):142
u:CA1_(Hippocampus):238
u:CA2_(Hippocampus):116
u:CA3_(Hippocampus):168
u:DG_(Hippocampus):150
u:Dorsal_Dentate_Nucleus:235
u:Entorhinal_Cortex:229
u:Fastigii_Nucleus:255
u:HATA_Region:174
u:Lobule_I_IV_(Hem):215
u:Lobule_IX_(Hem):134
u:Lobule_IX_(Verm):209
u:Lobule_V_(Hem):247
u:Lobule_VI_(Hem):222
u:Lobule_VI_(Verm):112
u:Lobule_VIIIa_(Hem):207
u:Lobule_VIIIa_(Verm):182
u:Lobule_VIIIb_(Hem):196
u:Lobule_VIIIb_(Verm):154
u:Lobule_VIIa_crusI_(Hem):212
u:Lobule_VIIa_crusI_(Verm):137
u:Lobule_VIIa_crusII_(Hem):216
u:Lobule_VIIa_crusII_(Verm):140
u:Lobule_VIIb_(Hem):164
u:Lobule_VIIb_(Verm):205
u:Lobule_X_(Hem):221
u:Lobule_X_(Verm):184
u:Subiculum:244
u:Thal:_Motor:176
u:Thal:_Parietal:179
u:Thal:_Prefrontal:156
u:Thal:_Premotor:188
u:Thal:_Somatosensory:190
u:Thal:_Temporal:232
u:Thal:_Visual:227
u:Ventral_Dentate_Nucleus:195
----------- End regions for CA_MPM_22_MNI atlas --------------

Atlas CA_MPM_22_TT,      100 regions
----------- Begin regions for CA_MPM_22_TT atlas-----------
u:Interposed_Nucleus :111
u:Amygdala_(AStr) :193
u:Amygdala_(CM) :133
u:Amygdala_(LB) :202
u:Amygdala_(SF) :151
u:Area_FG3 :117
u:Area_1 :106
u:Area_2 :243
u:Area_25 :178
u:Area_33 :119
u:Area_3a :250
u:Area_3b :187
u:Area_44 :246
u:Area_45 :129
u:Area_4a :160
u:Area_4p :191
u:Area_5Ci_(SPL) :185
u:Area_5L_(SPL) :159
u:Area_5M_(SPL) :241
u:Area_7A_(SPL) :165
u:Area_7M_(SPL) :120
u:Area_7P_(SPL) :224
u:Area_7PC_(SPL) :167
u:Area_FG1 :148
u:Area_FG2 :171
u:Area_FG4 :123
u:Area_Fo1 :170
u:Area_Fo2 :109
u:Area_Fo3 :145
u:Area_Fp1 :219
u:Area_Fp2 :230
u:Area_Id1 :126
u:Area_Ig1 :236
u:Area_Ig2 :204
u:Area_OP1_(SII) :122
u:Area_OP2_(PIVC) :139
u:Area_OP3_(VS) :147
u:Area_OP4_(PV) :173
u:Area_PF_(IPL) :136
u:Area_PFcm_(IPL) :153
u:Area_PFm_(IPL) :128
u:Area_PFop_(IPL) :125
u:Area_PFt_(IPL) :240
u:Area_PGa_(IPL) :201
u:Area_PGp_(IPL) :198
u:Area_TE_1.0 :210
u:Area_TE_1.1 :213
u:Area_TE_1.2 :218
u:Area_TE_3 :181
u:Area_hIP1_(IPS) :131
u:Area_hIP2_(IPS) :226
u:Area_hIP3_(IPS) :157
u:Area_hOc1_(V1) :249
u:Area_hOc2_(V2) :252
u:Area_hOc3d_(V3d) :199
u:Area_hOc3v_(V3v) :108
u:Area_hOc4d_(V3A) :143
u:Area_hOc4la :162
u:Area_hOc4lp :233
u:Area_hOc4v_(V4(v)) :103
u:Area_hOc5_(V5/MT) :105
u:Area_s24 :253
u:Area_s32 :102
u:BF_(Ch_1-3) :114
u:BF_(Ch_4) :142
u:CA1_(Hippocampus) :238
u:CA2_(Hippocampus) :116
u:CA3_(Hippocampus) :168
u:DG_(Hippocampus) :150
u:Dorsal_Dentate_Nucleus :235
u:Entorhinal_Cortex :229
u:Fastigii_Nucleus :255
u:HATA_Region :174
u:Lobule_I_IV_(Hem) :215
u:Lobule_IX_(Hem) :134
u:Lobule_IX_(Verm) :209
u:Lobule_V_(Hem) :247
u:Lobule_VI_(Hem) :222
u:Lobule_VI_(Verm) :112
u:Lobule_VIIIa_(Hem) :207
u:Lobule_VIIIa_(Verm) :182
u:Lobule_VIIIb_(Hem) :196
u:Lobule_VIIIb_(Verm) :154
u:Lobule_VIIa_crusI_(Hem) :212
u:Lobule_VIIa_crusI_(Verm) :137
u:Lobule_VIIa_crusII_(Hem) :216
u:Lobule_VIIa_crusII_(Verm) :140
u:Lobule_VIIb_(Hem) :164
u:Lobule_VIIb_(Verm) :205
u:Lobule_X_(Hem) :221
u:Lobule_X_(Verm) :184
u:Subiculum :244
u:Thal:_Motor :176
u:Thal:_Parietal :179
u:Thal:_Prefrontal :156
u:Thal:_Premotor :188
u:Thal:_Somatosensory :190
u:Thal:_Temporal :232
u:Thal:_Visual :227
u:Ventral_Dentate_Nucleus :195
----------- End regions for CA_MPM_22_TT atlas --------------

Atlas CA_N27_ML,      115 regions
----------- Begin regions for CA_N27_ML atlas-----------
l:Left Precentral Gyrus:1  
r:Right Precentral Gyrus:2  
l:Left Superior Frontal Gyrus:3  
r:Right Superior Frontal Gyrus:4  
l:Left Superior Orbital Gyrus:5  
r:Right Superior Orbital Gyrus:6  
l:Left Middle Frontal Gyrus:7  
r:Right Middle Frontal Gyrus:8  
l:Left Middle Orbital Gyrus:9  
r:Right Middle Orbital Gyrus:10 
l:Left Inferior Frontal Gyrus (p. Opercularis):11 
r:Right Inferior Frontal Gyrus (p. Opercularis):12 
l:Left Inferior Frontal Gyrus (p. Triangularis):13 
r:Right Inferior Frontal Gyrus (p. Triangularis):14 
l:Left Inferior Frontal Gyrus (p. Orbitalis):15 
r:Right Inferior Frontal Gyrus (p. Orbitalis):16 
l:Left Rolandic Operculum:17 
r:Right Rolandic Operculum:18 
l:Left SMA:19 
r:Right SMA:20 
l:Left Olfactory cortex:21 
r:Right Olfactory cortex:22 
l:Left Superior Medial Gyrus:23 
r:Right Superior Medial Gyrus:24 
l:Left Mid Orbital Gyrus:25 
r:Right Mid Orbital Gyrus:26 
l:Left Rectal Gyrus:27 
r:Right Rectal Gyrus:28 
l:Left Insula Lobe:29 
r:Right Insula Lobe:30 
l:Left Anterior Cingulate Cortex:31 
r:Right Anterior Cingulate Cortex:32 
l:Left Middle Cingulate Cortex:33 
r:Right Middle Cingulate Cortex:34 
l:Left Posterior Cingulate Cortex:35 
r:Right Posterior Cingulate Cortex:36 
l:Left Hippocampus:37 
r:Right Hippocampus:38 
l:Left ParaHippocampal Gyrus:39 
r:Right ParaHippocampal Gyrus:40 
l:Left Amygdala:41 
r:Right Amygdala:42 
l:Left Calcarine Gyrus:43 
r:Right Calcarine Gyrus:44 
l:Left Cuneus:45 
r:Right Cuneus:46 
l:Left Lingual Gyrus:47 
r:Right Lingual Gyrus:48 
l:Left Superior Occipital Gyrus:49 
r:Right Superior Occipital Gyrus:50 
l:Left Middle Occipital Gyrus:51 
r:Right Middle Occipital Gyrus:52 
l:Left Inferior Occipital Gyrus:53 
r:Right Inferior Occipital Gyrus:54 
l:Left Fusiform Gyrus:55 
r:Right Fusiform Gyrus:56 
l:Left Postcentral Gyrus:57 
r:Right Postcentral Gyrus:58 
l:Left Superior Parietal Lobule:59 
r:Right Superior Parietal Lobule:60 
l:Left Inferior Parietal Lobule:61 
r:Right Inferior Parietal Lobule:62 
l:Left SupraMarginal Gyrus:63 
r:Right SupraMarginal Gyrus:64 
l:Left Angular Gyrus:65 
r:Right Angular Gyrus:66 
l:Left Precuneus:67 
r:Right Precuneus:68 
l:Left Paracentral Lobule:69 
r:Right Paracentral Lobule:70 
l:Left Caudate Nucleus:71 
r:Right Caudate Nucleus:72 
l:Left Putamen:73 
r:Right Putamen:74 
l:Left Pallidum:75 
r:Right Pallidum:76 
l:Left Thalamus:77 
r:Right Thalamus:78 
l:Left Heschls Gyrus:79 
r:Right Heschls Gyrus:80 
l:Left Superior Temporal Gyrus:81 
r:Right Superior Temporal Gyrus:82 
l:Left Temporal Pole:83 
r:Right Temporal Pole:84 
l:Left Middle Temporal Gyrus:85 
r:Right Middle Temporal Gyrus:86 
l:Left Medial Temporal Pole:87 
r:Right Medial Temporal Pole:88 
l:Left Inferior Temporal Gyrus:89 
r:Right Inferior Temporal Gyrus:90 
l:Left Cerebellum (Crus 1):91 
r:Right Cerebellum (Crus 1):92 
l:Left Cerebellum (Crus 2):93 
r:Right Cerebellum (Crus 2):94 
l:Left Cerebellum (III):95 
r:Right Cerebellum (III):96 
l:Left Cerebellum (IV-V):97 
r:Right Cerebellum (IV-V):98 
l:Left Cerebellum (VI):99 
r:Right Cerebellum (VI):100
l:Left Cerebellum (VII):101
r:Right Cerebellum (VII):102
l:Left Cerebellum (VIII):103
r:Right Cerebellum (VIII):104
l:Left Cerebellum (IX):105
r:Right Cerebellum (IX):106
l:Left Cerebellum (X):107
r:Right Cerebellum (X):108
u:Cerebellar Vermis (1/2):109
u:Cerebellar Vermis (3):110
u:Cerebellar Vermis (4/5):111
u:Cerebellar Vermis (6):112
u:Cerebellar Vermis (7):113
u:Cerebellar Vermis (8):114
u:Cerebellar Vermis (9):115
----------- End regions for CA_N27_ML atlas --------------

Atlas CA_N27_MPM,      75 regions
----------- Begin regions for CA_N27_MPM atlas-----------
u:hIP1:103
u:SPL (7M):105
u:Lobule X (Hem):107
u:Lobule V:109
u:Th-Parietal:111
u:Hipp (FD):113
u:Amyg (SF):115
u:TE 1.1:117
u:Area 4p:119
u:Insula (Id1):121
u:Hipp (CA):123
u:hOC3v (V3v):125
u:IPC (PGa):127
u:TE 1.2:129
u:Area 44:131
u:Area 45:133
u:Area 4a:135
u:Amyg (LB):137
u:Insula (Ig1):140
u:Lobule IX (Vermis):142
u:SPL (5L):144
u:Th-Premotor:146
u:Insula (Ig2):148
u:Lobules I-IV (Hem):150
u:SPL (7A):152
u:TE 1.0:154
u:Area 2:156
u:Lobule VIIa Crus I (Vermis):158
u:Amyg (CM):160
u:hOC4v (V4):162
u:Lobule IX (Hem):164
u:Th-Temporal:166
u:Lobule VIIIb (Hem):168
u:Lobule VI (Hem):170
u:Hipp (HATA):172
u:Th-Prefrontal:174
u:Area 6:176
u:TE 3:179
u:Area 17:181
u:OP 2:183
u:Lobule VIIIa (Vermis):185
u:Th-Somatosensory:187
u:IPC (PFm):189
u:Lobule X (Vermis):191
u:hOC5 (V5):193
u:Lobule VIIa Crus II (Vermis):195
u:Hipp (SUB):197
u:Lobule VI (Vermis):199
u:OP 1:201
u:SPL (5Ci):203
u:Lobule VIIa Crus II (Hem):205
u:hIP3:207
u:Lobule VIIIa (Hem):209
u:Th-Visual:211
u:Hipp (EC):213
u:IPC (PFt):215
u:Area 3b:218
u:Lobule VIIb (Vermis):220
u:Lobule VIIb (Hem):222
u:IPC (PFcm):224
u:IPC (PF):226
u:hIP2:228
u:SPL (7P):230
u:SPL (5M):232
u:IPC (PGp):234
u:Lobule VIIIb (Vermis):236
u:Th-Motor:238
u:Area 18:240
u:OP 4:242
u:IPC (PFop):244
u:OP 3:246
u:Lobule VIIa Crus I (Hem):248
u:Area 3a:250
u:Area 1:252
u:SPL (7PC):254
----------- End regions for CA_N27_MPM atlas --------------

** ERROR: Failed to get CA_N27_PM
*+ WARNING: NULL atlas
** ERROR: NULL atlas

Atlas CA_N27_GW,      2 regions
----------- Begin regions for CA_N27_GW atlas-----------
u:grey:0  
u:white:1  
----------- End regions for CA_N27_GW atlas --------------

Atlas CA_N27_LR,      2 regions
----------- Begin regions for CA_N27_LR atlas-----------
r:Right Brain:1  
l:Left Brain:2  
----------- End regions for CA_N27_LR atlas --------------

Atlas CA_ML_18_MNI,      116 regions
----------- Begin regions for CA_ML_18_MNI atlas-----------
l:Left Precentral Gyrus:1  
r:Right Precentral Gyrus:2  
l:Left Superior Frontal Gyrus:3  
r:Right Superior Frontal Gyrus:4  
l:Left Superior Orbital Gyrus:5  
r:Right Superior Orbital Gyrus:6  
l:Left Middle Frontal Gyrus:7  
r:Right Middle Frontal Gyrus:8  
l:Left Middle Orbital Gyrus:9  
r:Right Middle Orbital Gyrus:10 
l:Left Inferior Frontal Gyrus (p. Opercularis):11 
r:Right Inferior Frontal Gyrus (p. Opercularis):12 
l:Left Inferior Frontal Gyrus (p. Triangularis):13 
r:Right Inferior Frontal Gyrus (p. Triangularis):14 
l:Left Inferior Frontal Gyrus (p. Orbitalis):15 
r:Right Inferior Frontal Gyrus (p. Orbitalis):16 
l:Left Rolandic Operculum:17 
r:Right Rolandic Operculum:18 
l:Left SMA:19 
r:Right SMA:20 
l:Left Olfactory cortex:21 
r:Right Olfactory cortex:22 
l:Left Superior Medial Gyrus:23 
r:Right Superior Medial Gyrus:24 
l:Left Mid Orbital Gyrus:25 
r:Right Mid Orbital Gyrus:26 
l:Left Rectal Gyrus:27 
r:Right Rectal Gyrus:28 
l:Left Insula Lobe:29 
r:Right Insula Lobe:30 
l:Left Anterior Cingulate Cortex:31 
r:Right Anterior Cingulate Cortex:32 
l:Left Middle Cingulate Cortex:33 
r:Right Middle Cingulate Cortex:34 
l:Left Posterior Cingulate Cortex:35 
r:Right Posterior Cingulate Cortex:36 
l:Left Hippocampus:37 
r:Right Hippocampus:38 
l:Left ParaHippocampal Gyrus:39 
r:Right ParaHippocampal Gyrus:40 
l:Left Amygdala:41 
r:Right Amygdala:42 
l:Left Calcarine Gyrus:43 
r:Right Calcarine Gyrus:44 
l:Left Cuneus:45 
r:Right Cuneus:46 
l:Left Lingual Gyrus:47 
r:Right Lingual Gyrus:48 
l:Left Superior Occipital Gyrus:49 
r:Right Superior Occipital Gyrus:50 
l:Left Middle Occipital Gyrus:51 
r:Right Middle Occipital Gyrus:52 
l:Left Inferior Occipital Gyrus:53 
r:Right Inferior Occipital Gyrus:54 
l:Left Fusiform Gyrus:55 
r:Right Fusiform Gyrus:56 
l:Left Postcentral Gyrus:57 
r:Right Postcentral Gyrus:58 
l:Left Superior Parietal Lobule:59 
r:Right Superior Parietal Lobule:60 
l:Left Inferior Parietal Lobule:61 
r:Right Inferior Parietal Lobule:62 
l:Left SupraMarginal Gyrus:63 
r:Right SupraMarginal Gyrus:64 
l:Left Angular Gyrus:65 
r:Right Angular Gyrus:66 
l:Left Precuneus:67 
r:Right Precuneus:68 
l:Left Paracentral Lobule:69 
r:Right Paracentral Lobule:70 
l:Left Caudate Nucleus:71 
r:Right Caudate Nucleus:72 
l:Left Putamen:73 
r:Right Putamen:74 
l:Left Pallidum:75 
r:Right Pallidum:76 
l:Left Thalamus:77 
r:Right Thalamus:78 
l:Left Heschls Gyrus:79 
r:Right Heschls Gyrus:80 
l:Left Superior Temporal Gyrus:81 
r:Right Superior Temporal Gyrus:82 
l:Left Temporal Pole:83 
r:Right Temporal Pole:84 
l:Left Middle Temporal Gyrus:85 
r:Right Middle Temporal Gyrus:86 
l:Left Medial Temporal Pole:87 
r:Right Medial Temporal Pole:88 
l:Left Inferior Temporal Gyrus:89 
r:Right Inferior Temporal Gyrus:90 
l:Left Cerebellum (Crus 1):91 
r:Right Cerebellum (Crus 1):92 
l:Left Cerebellum (Crus 2):93 
r:Right Cerebellum (Crus 2):94 
l:Left Cerebellum (III):95 
r:Right Cerebellum (III):96 
l:Left Cerebellum (IV-V):97 
r:Right Cerebellum (IV-V):98 
l:Left Cerebellum (VI):99 
r:Right Cerebellum (VI):100
l:Left Cerebellum (VII):101
r:Right Cerebellum (VII):102
l:Left Cerebellum (VIII):103
r:Right Cerebellum (VIII):104
l:Left Cerebellum (IX):105
r:Right Cerebellum (IX):106
l:Left Cerebellum (X):107
r:Right Cerebellum (X):108
u:Cerebellar Vermis (1/2):109
u:Cerebellar Vermis (3):110
u:Cerebellar Vermis (4/5):111
u:Cerebellar Vermis (6):112
u:Cerebellar Vermis (7):113
u:Cerebellar Vermis (8):114
u:Cerebellar Vermis (9):115
u:Cerebellar Vermis (10):116
----------- End regions for CA_ML_18_MNI atlas --------------

Atlas CA_MPM_18_MNI,      75 regions
----------- Begin regions for CA_MPM_18_MNI atlas-----------
u:hIP1:103
u:SPL (7M):105
u:Lobule X (Hem):107
u:Lobule V:109
u:Th-Parietal:111
u:Hipp (FD):113
u:Amyg (SF):115
u:TE 1.1:117
u:Area 4p:119
u:Insula (Id1):121
u:Hipp (CA):123
u:hOC3v (V3v):125
u:IPC (PGa):127
u:TE 1.2:129
u:Area 44:131
u:Area 45:133
u:Area 4a:135
u:Amyg (LB):137
u:Insula (Ig1):140
u:Lobule IX (Vermis):142
u:SPL (5L):144
u:Th-Premotor:146
u:Insula (Ig2):148
u:Lobules I-IV (Hem):150
u:SPL (7A):152
u:TE 1.0:154
u:Area 2:156
u:Lobule VIIa Crus I (Vermis):158
u:Amyg (CM):160
u:hOC4v (V4):162
u:Lobule IX (Hem):164
u:Th-Temporal:166
u:Lobule VIIIb (Hem):168
u:Lobule VI (Hem):170
u:Hipp (HATA):172
u:Th-Prefrontal:174
u:Area 6:176
u:TE 3:179
u:Area 17:181
u:OP 2:183
u:Lobule VIIIa (Vermis):185
u:Th-Somatosensory:187
u:IPC (PFm):189
u:Lobule X (Vermis):191
u:hOC5 (V5):193
u:Lobule VIIa Crus II (Vermis):195
u:Hipp (SUB):197
u:Lobule VI (Vermis):199
u:OP 1:201
u:SPL (5Ci):203
u:Lobule VIIa Crus II (Hem):205
u:hIP3:207
u:Lobule VIIIa (Hem):209
u:Th-Visual:211
u:Hipp (EC):213
u:IPC (PFt):215
u:Area 3b:218
u:Lobule VIIb (Vermis):220
u:Lobule VIIb (Hem):222
u:IPC (PFcm):224
u:IPC (PF):226
u:hIP2:228
u:SPL (7P):230
u:SPL (5M):232
u:IPC (PGp):234
u:Lobule VIIIb (Vermis):236
u:Th-Motor:238
u:Area 18:240
u:OP 4:242
u:IPC (PFop):244
u:OP 3:246
u:Lobule VIIa Crus I (Hem):248
u:Area 3a:250
u:Area 1:252
u:SPL (7PC):254
----------- End regions for CA_MPM_18_MNI atlas --------------

Atlas CA_LR_18_MNI,      2 regions
----------- Begin regions for CA_LR_18_MNI atlas-----------
r:Right Brain:1  
l:Left Brain:2  
----------- End regions for CA_LR_18_MNI atlas --------------

Atlas CA_ML_18_MNIA,      115 regions
----------- Begin regions for CA_ML_18_MNIA atlas-----------
l:Left Precentral Gyrus:1  
r:Right Precentral Gyrus:2  
l:Left Superior Frontal Gyrus:3  
r:Right Superior Frontal Gyrus:4  
l:Left Superior Orbital Gyrus:5  
r:Right Superior Orbital Gyrus:6  
l:Left Middle Frontal Gyrus:7  
r:Right Middle Frontal Gyrus:8  
l:Left Middle Orbital Gyrus:9  
r:Right Middle Orbital Gyrus:10 
l:Left Inferior Frontal Gyrus (p. Opercularis):11 
r:Right Inferior Frontal Gyrus (p. Opercularis):12 
l:Left Inferior Frontal Gyrus (p. Triangularis):13 
r:Right Inferior Frontal Gyrus (p. Triangularis):14 
l:Left Inferior Frontal Gyrus (p. Orbitalis):15 
r:Right Inferior Frontal Gyrus (p. Orbitalis):16 
l:Left Rolandic Operculum:17 
r:Right Rolandic Operculum:18 
l:Left SMA:19 
r:Right SMA:20 
l:Left Olfactory cortex:21 
r:Right Olfactory cortex:22 
l:Left Superior Medial Gyrus:23 
r:Right Superior Medial Gyrus:24 
l:Left Mid Orbital Gyrus:25 
r:Right Mid Orbital Gyrus:26 
l:Left Rectal Gyrus:27 
r:Right Rectal Gyrus:28 
l:Left Insula Lobe:29 
r:Right Insula Lobe:30 
l:Left Anterior Cingulate Cortex:31 
r:Right Anterior Cingulate Cortex:32 
l:Left Middle Cingulate Cortex:33 
r:Right Middle Cingulate Cortex:34 
l:Left Posterior Cingulate Cortex:35 
r:Right Posterior Cingulate Cortex:36 
l:Left Hippocampus:37 
r:Right Hippocampus:38 
l:Left ParaHippocampal Gyrus:39 
r:Right ParaHippocampal Gyrus:40 
l:Left Amygdala:41 
r:Right Amygdala:42 
l:Left Calcarine Gyrus:43 
r:Right Calcarine Gyrus:44 
l:Left Cuneus:45 
r:Right Cuneus:46 
l:Left Lingual Gyrus:47 
r:Right Lingual Gyrus:48 
l:Left Superior Occipital Gyrus:49 
r:Right Superior Occipital Gyrus:50 
l:Left Middle Occipital Gyrus:51 
r:Right Middle Occipital Gyrus:52 
l:Left Inferior Occipital Gyrus:53 
r:Right Inferior Occipital Gyrus:54 
l:Left Fusiform Gyrus:55 
r:Right Fusiform Gyrus:56 
l:Left Postcentral Gyrus:57 
r:Right Postcentral Gyrus:58 
l:Left Superior Parietal Lobule:59 
r:Right Superior Parietal Lobule:60 
l:Left Inferior Parietal Lobule:61 
r:Right Inferior Parietal Lobule:62 
l:Left SupraMarginal Gyrus:63 
r:Right SupraMarginal Gyrus:64 
l:Left Angular Gyrus:65 
r:Right Angular Gyrus:66 
l:Left Precuneus:67 
r:Right Precuneus:68 
l:Left Paracentral Lobule:69 
r:Right Paracentral Lobule:70 
l:Left Caudate Nucleus:71 
r:Right Caudate Nucleus:72 
l:Left Putamen:73 
r:Right Putamen:74 
l:Left Pallidum:75 
r:Right Pallidum:76 
l:Left Thalamus:77 
r:Right Thalamus:78 
l:Left Heschls Gyrus:79 
r:Right Heschls Gyrus:80 
l:Left Superior Temporal Gyrus:81 
r:Right Superior Temporal Gyrus:82 
l:Left Temporal Pole:83 
r:Right Temporal Pole:84 
l:Left Middle Temporal Gyrus:85 
r:Right Middle Temporal Gyrus:86 
l:Left Medial Temporal Pole:87 
r:Right Medial Temporal Pole:88 
l:Left Inferior Temporal Gyrus:89 
r:Right Inferior Temporal Gyrus:90 
l:Left Cerebellum (Crus 1):91 
r:Right Cerebellum (Crus 1):92 
l:Left Cerebellum (Crus 2):93 
r:Right Cerebellum (Crus 2):94 
l:Left Cerebellum (III):95 
r:Right Cerebellum (III):96 
l:Left Cerebellum (IV-V):97 
r:Right Cerebellum (IV-V):98 
l:Left Cerebellum (VI):99 
r:Right Cerebellum (VI):100
l:Left Cerebellum (VII):101
r:Right Cerebellum (VII):102
l:Left Cerebellum (VIII):103
r:Right Cerebellum (VIII):104
l:Left Cerebellum (IX):105
r:Right Cerebellum (IX):106
l:Left Cerebellum (X):107
r:Right Cerebellum (X):108
u:Cerebellar Vermis (1/2):109
u:Cerebellar Vermis (3):110
u:Cerebellar Vermis (4/5):111
u:Cerebellar Vermis (6):112
u:Cerebellar Vermis (7):113
u:Cerebellar Vermis (8):114
u:Cerebellar Vermis (9):115
----------- End regions for CA_ML_18_MNIA atlas --------------

Atlas CA_MPM_18_MNIA,      75 regions
----------- Begin regions for CA_MPM_18_MNIA atlas-----------
u:hIP1:103
u:SPL (7M):105
u:Lobule X (Hem):107
u:Lobule V:109
u:Th-Parietal:111
u:Hipp (FD):113
u:Amyg (SF):115
u:TE 1.1:117
u:Area 4p:119
u:Insula (Id1):121
u:Hipp (CA):123
u:hOC3v (V3v):125
u:IPC (PGa):127
u:TE 1.2:129
u:Area 44:131
u:Area 45:133
u:Area 4a:135
u:Amyg (LB):137
u:Insula (Ig1):140
u:Lobule IX (Vermis):142
u:SPL (5L):144
u:Th-Premotor:146
u:Insula (Ig2):148
u:Lobules I-IV (Hem):150
u:SPL (7A):152
u:TE 1.0:154
u:Area 2:156
u:Lobule VIIa Crus I (Vermis):158
u:Amyg (CM):160
u:hOC4v (V4):162
u:Lobule IX (Hem):164
u:Th-Temporal:166
u:Lobule VIIIb (Hem):168
u:Lobule VI (Hem):170
u:Hipp (HATA):172
u:Th-Prefrontal:174
u:Area 6:176
u:TE 3:179
u:Area 17:181
u:OP 2:183
u:Lobule VIIIa (Vermis):185
u:Th-Somatosensory:187
u:IPC (PFm):189
u:Lobule X (Vermis):191
u:hOC5 (V5):193
u:Lobule VIIa Crus II (Vermis):195
u:Hipp (SUB):197
u:Lobule VI (Vermis):199
u:OP 1:201
u:SPL (5Ci):203
u:Lobule VIIa Crus II (Hem):205
u:hIP3:207
u:Lobule VIIIa (Hem):209
u:Th-Visual:211
u:Hipp (EC):213
u:IPC (PFt):215
u:Area 3b:218
u:Lobule VIIb (Vermis):220
u:Lobule VIIb (Hem):222
u:IPC (PFcm):224
u:IPC (PF):226
u:hIP2:228
u:SPL (7P):230
u:SPL (5M):232
u:IPC (PGp):234
u:Lobule VIIIb (Vermis):236
u:Th-Motor:238
u:Area 18:240
u:OP 4:242
u:IPC (PFop):244
u:OP 3:246
u:Lobule VIIa Crus I (Hem):248
u:Area 3a:250
u:Area 1:252
u:SPL (7PC):254
----------- End regions for CA_MPM_18_MNIA atlas --------------

** ERROR: Failed to get CA_PM_18_MNIA
*+ WARNING: NULL atlas
** ERROR: NULL atlas

Atlas CA_GW_18_MNIA,      2 regions
----------- Begin regions for CA_GW_18_MNIA atlas-----------
u:grey:0  
u:white:1  
----------- End regions for CA_GW_18_MNIA atlas --------------

Atlas CA_LR_18_MNIA,      2 regions
----------- Begin regions for CA_LR_18_MNIA atlas-----------
r:Right Brain:1  
l:Left Brain:2  
----------- End regions for CA_LR_18_MNIA atlas --------------

** ERROR: Failed to get DKD_Desai_PM
*+ WARNING: NULL atlas
** ERROR: NULL atlas
** ERROR: Failed to get DD_Desai_PM
*+ WARNING: NULL atlas
** ERROR: NULL atlas
** ERROR: Failed to get FS_Desai_PM
*+ WARNING: NULL atlas
** ERROR: NULL atlas

Atlas DD_Desai_MPM,      190 regions
----------- Begin regions for DD_Desai_MPM atlas-----------
u:ctx_lh_G_and_S_frontomargin:1  
u:ctx_lh_G_and_S_occipital_inf:2  
u:ctx_lh_G_and_S_paracentral:3  
u:ctx_lh_G_and_S_subcentral:4  
u:ctx_lh_G_and_S_transv_frontopol:5  
u:ctx_lh_G_and_S_cingul-Ant:6  
u:ctx_lh_G_and_S_cingul-Mid-Ant:7  
u:ctx_lh_G_and_S_cingul-Mid-Post:8  
u:ctx_lh_G_cingul-Post-dorsal:9  
u:ctx_lh_G_cingul-Post-ventral:10 
u:ctx_lh_G_cuneus:11 
u:ctx_lh_G_front_inf-Opercular:12 
u:ctx_lh_G_front_inf-Orbital:13 
u:ctx_lh_G_front_inf-Triangul:14 
u:ctx_lh_G_front_middle:15 
u:ctx_lh_G_front_sup:16 
u:ctx_lh_G_Ins_lg_and_S_cent_ins:17 
u:ctx_lh_G_insular_short:18 
u:ctx_lh_G_occipital_middle:19 
u:ctx_lh_G_occipital_sup:20 
u:ctx_lh_G_oc-temp_lat-fusifor:21 
u:ctx_lh_G_oc-temp_med-Lingual:22 
u:ctx_lh_G_oc-temp_med-Parahip:23 
u:ctx_lh_G_orbital:24 
u:ctx_lh_G_pariet_inf-Angular:25 
u:ctx_lh_G_pariet_inf-Supramar:26 
u:ctx_lh_G_parietal_sup:27 
u:ctx_lh_G_postcentral:28 
u:ctx_lh_G_precentral:29 
u:ctx_lh_G_precuneus:30 
u:ctx_lh_G_rectus:31 
u:ctx_lh_G_subcallosal:32 
u:ctx_lh_G_temp_sup-G_T_transv:33 
u:ctx_lh_G_temp_sup-Lateral:34 
u:ctx_lh_G_temp_sup-Plan_polar:35 
u:ctx_lh_G_temp_sup-Plan_tempo:36 
u:ctx_lh_G_temporal_inf:37 
u:ctx_lh_G_temporal_middle:38 
u:ctx_lh_Lat_Fis-ant-Horizont:39 
u:ctx_lh_Lat_Fis-ant-Vertical:40 
u:ctx_lh_Lat_Fis-post:41 
u:ctx_lh_Medial_wall:42 
u:ctx_lh_Pole_occipital:43 
u:ctx_lh_Pole_temporal:44 
u:ctx_lh_S_calcarine:45 
u:ctx_lh_S_central:46 
u:ctx_lh_S_cingul-Marginalis:47 
u:ctx_lh_S_circular_insula_ant:48 
u:ctx_lh_S_circular_insula_inf:49 
u:ctx_lh_S_circular_insula_sup:50 
u:ctx_lh_S_collat_transv_ant:51 
u:ctx_lh_S_collat_transv_post:52 
u:ctx_lh_S_front_inf:53 
u:ctx_lh_S_front_middle:54 
u:ctx_lh_S_front_sup:55 
u:ctx_lh_S_interm_prim-Jensen:56 
u:ctx_lh_S_intrapariet_and_P_trans:57 
u:ctx_lh_S_oc_middle_and_Lunatus:58 
u:ctx_lh_S_oc_sup_and_transversal:59 
u:ctx_lh_S_occipital_ant:60 
u:ctx_lh_S_oc-temp_lat:61 
u:ctx_lh_S_oc-temp_med_and_Lingual:62 
u:ctx_lh_S_orbital_lateral:63 
u:ctx_lh_S_orbital_med-olfact:64 
u:ctx_lh_S_orbital-H_Shaped:65 
u:ctx_lh_S_parieto_occipital:66 
u:ctx_lh_S_pericallosal:67 
u:ctx_lh_S_postcentral:68 
u:ctx_lh_S_precentral-inf-part:69 
u:ctx_lh_S_precentral-sup-part:70 
u:ctx_lh_S_suborbital:71 
u:ctx_lh_S_subparietal:72 
u:ctx_lh_S_temporal_inf:73 
u:ctx_lh_S_temporal_sup:74 
u:ctx_lh_S_temporal_transverse:75 
u:ctx_rh_G_and_S_frontomargin:76 
u:ctx_rh_G_and_S_occipital_inf:77 
u:ctx_rh_G_and_S_paracentral:78 
u:ctx_rh_G_and_S_subcentral:79 
u:ctx_rh_G_and_S_transv_frontopol:80 
u:ctx_rh_G_and_S_cingul-Ant:81 
u:ctx_rh_G_and_S_cingul-Mid-Ant:82 
u:ctx_rh_G_and_S_cingul-Mid-Post:83 
u:ctx_rh_G_cingul-Post-dorsal:84 
u:ctx_rh_G_cingul-Post-ventral:85 
u:ctx_rh_G_cuneus:86 
u:ctx_rh_G_front_inf-Opercular:87 
u:ctx_rh_G_front_inf-Orbital:88 
u:ctx_rh_G_front_inf-Triangul:89 
u:ctx_rh_G_front_middle:90 
u:ctx_rh_G_front_sup:91 
u:ctx_rh_G_Ins_lg_and_S_cent_ins:92 
u:ctx_rh_G_insular_short:93 
u:ctx_rh_G_occipital_middle:94 
u:ctx_rh_G_occipital_sup:95 
u:ctx_rh_G_oc-temp_lat-fusifor:96 
u:ctx_rh_G_oc-temp_med-Lingual:97 
u:ctx_rh_G_oc-temp_med-Parahip:98 
u:ctx_rh_G_orbital:99 
u:ctx_rh_G_pariet_inf-Angular:100
u:ctx_rh_G_pariet_inf-Supramar:101
u:ctx_rh_G_parietal_sup:102
u:ctx_rh_G_postcentral:103
u:ctx_rh_G_precentral:104
u:ctx_rh_G_precuneus:105
u:ctx_rh_G_rectus:106
u:ctx_rh_G_subcallosal:107
u:ctx_rh_G_temp_sup-G_T_transv:108
u:ctx_rh_G_temp_sup-Lateral:109
u:ctx_rh_G_temp_sup-Plan_polar:110
u:ctx_rh_G_temp_sup-Plan_tempo:111
u:ctx_rh_G_temporal_inf:112
u:ctx_rh_G_temporal_middle:113
u:ctx_rh_Lat_Fis-ant-Horizont:114
u:ctx_rh_Lat_Fis-ant-Vertical:115
u:ctx_rh_Lat_Fis-post:116
u:ctx_rh_Medial_wall:117
u:ctx_rh_Pole_occipital:118
u:ctx_rh_Pole_temporal:119
u:ctx_rh_S_calcarine:120
u:ctx_rh_S_central:121
u:ctx_rh_S_cingul-Marginalis:122
u:ctx_rh_S_circular_insula_ant:123
u:ctx_rh_S_circular_insula_inf:124
u:ctx_rh_S_circular_insula_sup:125
u:ctx_rh_S_collat_transv_ant:126
u:ctx_rh_S_collat_transv_post:127
u:ctx_rh_S_front_inf:128
u:ctx_rh_S_front_middle:129
u:ctx_rh_S_front_sup:130
u:ctx_rh_S_interm_prim-Jensen:131
u:ctx_rh_S_intrapariet_and_P_trans:132
u:ctx_rh_S_oc_middle_and_Lunatus:133
u:ctx_rh_S_oc_sup_and_transversal:134
u:ctx_rh_S_occipital_ant:135
u:ctx_rh_S_oc-temp_lat:136
u:ctx_rh_S_oc-temp_med_and_Lingual:137
u:ctx_rh_S_orbital_lateral:138
u:ctx_rh_S_orbital_med-olfact:139
u:ctx_rh_S_orbital-H_Shaped:140
u:ctx_rh_S_parieto_occipital:141
u:ctx_rh_S_pericallosal:142
u:ctx_rh_S_postcentral:143
u:ctx_rh_S_precentral-inf-part:144
u:ctx_rh_S_precentral-sup-part:145
u:ctx_rh_S_suborbital:146
u:ctx_rh_S_subparietal:147
u:ctx_rh_S_temporal_inf:148
u:ctx_rh_S_temporal_sup:149
u:ctx_rh_S_temporal_transverse:150
l:Left-Cerebral-White-Matter:151
l:Left-Lateral-Ventricle:152
l:Left-Inf-Lat-Vent:153
l:Left-Cerebellum-White-Matter:154
l:Left-Cerebellum-Cortex:155
l:Left-Thalamus-Proper:156
l:Left-Caudate:157
l:Left-Putamen:158
l:Left-Pallidum:159
u:3rd-Ventricle:160
u:4th-Ventricle:161
u:Brain-Stem:162
l:Left-Hippocampus:163
l:Left-Amygdala:164
l:Left-Accumbens-area:165
l:Left-VentralDC:166
l:Left-vessel:167
l:Left-choroid-plexus:168
r:Right-Cerebral-White-Matter:169
r:Right-Lateral-Ventricle:170
r:Right-Inf-Lat-Vent:171
r:Right-Cerebellum-White-Matter:172
r:Right-Cerebellum-Cortex:173
r:Right-Thalamus-Proper:174
r:Right-Caudate:175
r:Right-Putamen:176
r:Right-Pallidum:177
r:Right-Hippocampus:178
r:Right-Amygdala:179
r:Right-Accumbens-area:180
r:Right-VentralDC:181
r:Right-vessel:182
r:Right-choroid-plexus:183
u:5th-Ventricle:184
u:Optic-Chiasm:185
u:CC_Posterior:186
u:CC_Mid_Posterior:187
u:CC_Central:188
u:CC_Mid_Anterior:189
u:CC_Anterior:190
----------- End regions for DD_Desai_MPM atlas --------------

Atlas DKD_Desai_MPM,      110 regions
----------- Begin regions for DKD_Desai_MPM atlas-----------
u:ctx-lh-bankssts:1  
u:ctx-lh-caudalanteriorcingulate:2  
u:ctx-lh-caudalmiddlefrontal:3  
u:ctx-lh-corpuscallosum:4  
u:ctx-lh-cuneus:5  
u:ctx-lh-entorhinal:6  
u:ctx-lh-fusiform:7  
u:ctx-lh-inferiorparietal:8  
u:ctx-lh-inferiortemporal:9  
u:ctx-lh-isthmuscingulate:10 
u:ctx-lh-lateraloccipital:11 
u:ctx-lh-lateralorbitofrontal:12 
u:ctx-lh-lingual:13 
u:ctx-lh-medialorbitofrontal:14 
u:ctx-lh-middletemporal:15 
u:ctx-lh-parahippocampal:16 
u:ctx-lh-paracentral:17 
u:ctx-lh-parsopercularis:18 
u:ctx-lh-parsorbitalis:19 
u:ctx-lh-parstriangularis:20 
u:ctx-lh-pericalcarine:21 
u:ctx-lh-postcentral:22 
u:ctx-lh-posteriorcingulate:23 
u:ctx-lh-precentral:24 
u:ctx-lh-precuneus:25 
u:ctx-lh-rostralanteriorcingulate:26 
u:ctx-lh-rostralmiddlefrontal:27 
u:ctx-lh-superiorfrontal:28 
u:ctx-lh-superiorparietal:29 
u:ctx-lh-superiortemporal:30 
u:ctx-lh-supramarginal:31 
u:ctx-lh-frontalpole:32 
u:ctx-lh-temporalpole:33 
u:ctx-lh-transversetemporal:34 
u:ctx-lh-insula:35 
u:ctx-rh-bankssts:36 
u:ctx-rh-caudalanteriorcingulate:37 
u:ctx-rh-caudalmiddlefrontal:38 
u:ctx-rh-corpuscallosum:39 
u:ctx-rh-cuneus:40 
u:ctx-rh-entorhinal:41 
u:ctx-rh-fusiform:42 
u:ctx-rh-inferiorparietal:43 
u:ctx-rh-inferiortemporal:44 
u:ctx-rh-isthmuscingulate:45 
u:ctx-rh-lateraloccipital:46 
u:ctx-rh-lateralorbitofrontal:47 
u:ctx-rh-lingual:48 
u:ctx-rh-medialorbitofrontal:49 
u:ctx-rh-middletemporal:50 
u:ctx-rh-parahippocampal:51 
u:ctx-rh-paracentral:52 
u:ctx-rh-parsopercularis:53 
u:ctx-rh-parsorbitalis:54 
u:ctx-rh-parstriangularis:55 
u:ctx-rh-pericalcarine:56 
u:ctx-rh-postcentral:57 
u:ctx-rh-posteriorcingulate:58 
u:ctx-rh-precentral:59 
u:ctx-rh-precuneus:60 
u:ctx-rh-rostralanteriorcingulate:61 
u:ctx-rh-rostralmiddlefrontal:62 
u:ctx-rh-superiorfrontal:63 
u:ctx-rh-superiorparietal:64 
u:ctx-rh-superiortemporal:65 
u:ctx-rh-supramarginal:66 
u:ctx-rh-frontalpole:67 
u:ctx-rh-temporalpole:68 
u:ctx-rh-transversetemporal:69 
u:ctx-rh-insula:70 
l:Left-Cerebral-White-Matter:71 
l:Left-Lateral-Ventricle:72 
l:Left-Inf-Lat-Vent:73 
l:Left-Cerebellum-White-Matter:74 
l:Left-Cerebellum-Cortex:75 
l:Left-Thalamus-Proper:76 
l:Left-Caudate:77 
l:Left-Putamen:78 
l:Left-Pallidum:79 
u:3rd-Ventricle:80 
u:4th-Ventricle:81 
u:Brain-Stem:82 
l:Left-Hippocampus:83 
l:Left-Amygdala:84 
l:Left-Accumbens-area:85 
l:Left-VentralDC:86 
l:Left-vessel:87 
l:Left-choroid-plexus:88 
r:Right-Cerebral-White-Matter:89 
r:Right-Lateral-Ventricle:90 
r:Right-Inf-Lat-Vent:91 
r:Right-Cerebellum-White-Matter:92 
r:Right-Cerebellum-Cortex:93 
r:Right-Thalamus-Proper:94 
r:Right-Caudate:95 
r:Right-Putamen:96 
r:Right-Pallidum:97 
r:Right-Hippocampus:98 
r:Right-Amygdala:99 
r:Right-Accumbens-area:100
r:Right-VentralDC:101
r:Right-vessel:102
r:Right-choroid-plexus:103
u:5th-Ventricle:104
u:Optic-Chiasm:105
u:CC_Posterior:106
u:CC_Mid_Posterior:107
u:CC_Central:108
u:CC_Mid_Anterior:109
u:CC_Anterior:110
----------- End regions for DKD_Desai_MPM atlas --------------


Atlas MNI_VmPFC,      16 regions
----------- Begin regions for MNI_VmPFC atlas-----------
u:area11m_left:1  
u:area11m_right:2  
u:area14c_left:3  
u:area14c_right:4  
u:area14m_left:5  
u:area14m_right:6  
u:area14r_left:7  
u:area14r_right:8  
u:area14rr_left:9  
u:area14rr_right:10 
u:area24_left:11 
u:area24_right:12 
u:area25_left:13 
u:area25_right:14 
u:area32_left:15 
u:area32_right:16 
----------- End regions for MNI_VmPFC atlas --------------

Atlas TT_Daemon,      241 regions
----------- Begin regions for TT_Daemon atlas-----------
u:Anterior Commissure:1  
u:Posterior Commissure:2  
u:Corpus Callosum:3  
l:Left  Hippocampus:268
r:Right Hippocampus:68 
l:Left  Amygdala:271
r:Right Amygdala:71 
l:Left  Posterior Cingulate:220
r:Right Posterior Cingulate:20 
l:Left  Anterior Cingulate:221
r:Right Anterior Cingulate:21 
l:Left  Subcallosal Gyrus:222
r:Right Subcallosal Gyrus:22 
l:Left  Transverse Temporal Gyrus:224
r:Right Transverse Temporal Gyrus:24 
l:Left  Uncus:225
r:Right Uncus:25 
l:Left  Rectal Gyrus:226
r:Right Rectal Gyrus:26 
l:Left  Fusiform Gyrus:227
r:Right Fusiform Gyrus:27 
l:Left  Inferior Occipital Gyrus:228
r:Right Inferior Occipital Gyrus:28 
l:Left  Inferior Temporal Gyrus:229
r:Right Inferior Temporal Gyrus:29 
l:Left  Insula:230
r:Right Insula:30 
l:Left  Parahippocampal Gyrus:231
r:Right Parahippocampal Gyrus:31 
l:Left  Lingual Gyrus:232
r:Right Lingual Gyrus:32 
l:Left  Middle Occipital Gyrus:233
r:Right Middle Occipital Gyrus:33 
l:Left  Orbital Gyrus:234
r:Right Orbital Gyrus:34 
l:Left  Middle Temporal Gyrus:235
r:Right Middle Temporal Gyrus:35 
l:Left  Superior Temporal Gyrus:236
r:Right Superior Temporal Gyrus:36 
l:Left  Superior Occipital Gyrus:237
r:Right Superior Occipital Gyrus:37 
l:Left  Inferior Frontal Gyrus:239
r:Right Inferior Frontal Gyrus:39 
l:Left  Cuneus:240
r:Right Cuneus:40 
l:Left  Angular Gyrus:241
r:Right Angular Gyrus:41 
l:Left  Supramarginal Gyrus:242
r:Right Supramarginal Gyrus:42 
l:Left  Cingulate Gyrus:243
r:Right Cingulate Gyrus:43 
l:Left  Inferior Parietal Lobule:244
r:Right Inferior Parietal Lobule:44 
l:Left  Precuneus:245
r:Right Precuneus:45 
l:Left  Superior Parietal Lobule:246
r:Right Superior Parietal Lobule:46 
l:Left  Middle Frontal Gyrus:247
r:Right Middle Frontal Gyrus:47 
l:Left  Paracentral Lobule:248
r:Right Paracentral Lobule:48 
l:Left  Postcentral Gyrus:249
r:Right Postcentral Gyrus:49 
l:Left  Precentral Gyrus:250
r:Right Precentral Gyrus:50 
l:Left  Superior Frontal Gyrus:251
r:Right Superior Frontal Gyrus:51 
l:Left  Medial Frontal Gyrus:252
r:Right Medial Frontal Gyrus:52 
l:Left  Lentiform Nucleus:270
r:Right Lentiform Nucleus:70 
l:Left  Hypothalamus:272
r:Right Hypothalamus:72 
l:Left  Red Nucleus:273
r:Right Red Nucleus:73 
l:Left  Substantia Nigra:274
r:Right Substantia Nigra:74 
l:Left  Claustrum:275
r:Right Claustrum:75 
l:Left  Thalamus:276
r:Right Thalamus:76 
l:Left  Caudate:277
r:Right Caudate:77 
l:Left  Caudate Tail:324
r:Right Caudate Tail:124
l:Left  Caudate Body:325
r:Right Caudate Body:125
l:Left  Caudate Head:326
r:Right Caudate Head:126
l:Left  Ventral Anterior Nucleus:328
r:Right Ventral Anterior Nucleus:128
l:Left  Ventral Posterior Medial Nucleus:329
r:Right Ventral Posterior Medial Nucleus:129
l:Left  Ventral Posterior Lateral Nucleus:330
r:Right Ventral Posterior Lateral Nucleus:130
l:Left  Medial Dorsal Nucleus:331
r:Right Medial Dorsal Nucleus:131
l:Left  Lateral Dorsal Nucleus:332
r:Right Lateral Dorsal Nucleus:132
l:Left  Pulvinar:333
r:Right Pulvinar:133
l:Left  Lateral Posterior Nucleus:334
r:Right Lateral Posterior Nucleus:134
l:Left  Ventral Lateral Nucleus:335
r:Right Ventral Lateral Nucleus:135
l:Left  Midline Nucleus:336
r:Right Midline Nucleus:136
l:Left  Anterior Nucleus:337
r:Right Anterior Nucleus:137
l:Left  Mammillary Body:338
r:Right Mammillary Body:138
l:Left  Medial Globus Pallidus:344
r:Right Medial Globus Pallidus:144
l:Left  Lateral Globus Pallidus:345
r:Right Lateral Globus Pallidus:145
l:Left  Putamen:351
r:Right Putamen:151
l:Left  Nucleus Accumbens:346
r:Right Nucleus Accumbens:146
l:Left  Medial Geniculum Body:347
r:Right Medial Geniculum Body:147
l:Left  Lateral Geniculum Body:348
r:Right Lateral Geniculum Body:148
l:Left  Subthalamic Nucleus:349
r:Right Subthalamic Nucleus:149
l:Left  Brodmann area 1:281
r:Right Brodmann area 1:81 
l:Left  Brodmann area 2:282
r:Right Brodmann area 2:82 
l:Left  Brodmann area 3:283
r:Right Brodmann area 3:83 
l:Left  Brodmann area 4:284
r:Right Brodmann area 4:84 
l:Left  Brodmann area 5:285
r:Right Brodmann area 5:85 
l:Left  Brodmann area 6:286
r:Right Brodmann area 6:86 
l:Left  Brodmann area 7:287
r:Right Brodmann area 7:87 
l:Left  Brodmann area 8:288
r:Right Brodmann area 8:88 
l:Left  Brodmann area 9:289
r:Right Brodmann area 9:89 
l:Left  Brodmann area 10:290
r:Right Brodmann area 10:90 
l:Left  Brodmann area 11:291
r:Right Brodmann area 11:91 
l:Left  Brodmann area 13:293
r:Right Brodmann area 13:93 
l:Left  Brodmann area 17:294
r:Right Brodmann area 17:94 
l:Left  Brodmann area 18:295
r:Right Brodmann area 18:95 
l:Left  Brodmann area 19:296
r:Right Brodmann area 19:96 
l:Left  Brodmann area 20:297
r:Right Brodmann area 20:97 
l:Left  Brodmann area 21:298
r:Right Brodmann area 21:98 
l:Left  Brodmann area 22:299
r:Right Brodmann area 22:99 
l:Left  Brodmann area 23:300
r:Right Brodmann area 23:100
l:Left  Brodmann area 24:301
r:Right Brodmann area 24:101
l:Left  Brodmann area 25:302
r:Right Brodmann area 25:102
l:Left  Brodmann area 27:303
r:Right Brodmann area 27:103
l:Left  Brodmann area 28:304
r:Right Brodmann area 28:104
l:Left  Brodmann area 29:305
r:Right Brodmann area 29:105
l:Left  Brodmann area 30:306
r:Right Brodmann area 30:106
l:Left  Brodmann area 31:307
r:Right Brodmann area 31:107
l:Left  Brodmann area 32:308
r:Right Brodmann area 32:108
l:Left  Brodmann area 33:309
r:Right Brodmann area 33:109
l:Left  Brodmann area 34:310
r:Right Brodmann area 34:110
l:Left  Brodmann area 35:311
r:Right Brodmann area 35:111
l:Left  Brodmann area 36:312
r:Right Brodmann area 36:112
l:Left  Brodmann area 37:313
r:Right Brodmann area 37:113
l:Left  Brodmann area 38:314
r:Right Brodmann area 38:114
l:Left  Brodmann area 39:315
r:Right Brodmann area 39:115
l:Left  Brodmann area 40:316
r:Right Brodmann area 40:116
l:Left  Brodmann area 41:317
r:Right Brodmann area 41:117
l:Left  Brodmann area 42:318
r:Right Brodmann area 42:118
l:Left  Brodmann area 43:319
r:Right Brodmann area 43:119
l:Left  Brodmann area 44:320
r:Right Brodmann area 44:120
l:Left  Brodmann area 45:321
r:Right Brodmann area 45:121
l:Left  Brodmann area 46:322
r:Right Brodmann area 46:122
l:Left  Brodmann area 47:323
r:Right Brodmann area 47:123
l:Left  Uvula of Vermis:253
r:Right Uvula of Vermis:53 
l:Left  Pyramis of Vermis:254
r:Right Pyramis of Vermis:54 
l:Left  Tuber of Vermis:255
r:Right Tuber of Vermis:55 
l:Left  Declive of Vermis:256
r:Right Declive of Vermis:56 
l:Left  Culmen of Vermis:257
r:Right Culmen of Vermis:57 
l:Left  Cerebellar Tonsil:258
r:Right Cerebellar Tonsil:58 
l:Left  Inferior Semi-Lunar Lobule:259
r:Right Inferior Semi-Lunar Lobule:59 
l:Left  Fastigium:260
r:Right Fastigium:60 
l:Left  Nodule:261
r:Right Nodule:61 
l:Left  Uvula:262
r:Right Uvula:62 
l:Left  Pyramis:263
r:Right Pyramis:63 
l:Left  Culmen:266
r:Right Culmen:66 
l:Left  Declive:265
r:Right Declive:65 
l:Left  Dentate:327
r:Right Dentate:127
l:Left  Tuber:264
r:Right Tuber:64 
l:Left  Cerebellar Lingual:267
r:Right Cerebellar Lingual:67 
----------- End regions for TT_Daemon atlas --------------

Atlas Haskins_Pediatric_Nonlinear_1.0,      107 regions
----------- Begin regions for Haskins_Pediatric_Nonlinear_1.0 atlas-----------
l:Left-Lateral-Ventricle:1  
l:Left-Inf-Lat-Vent:2  
l:Left-Cerebellum-White-Matter:3  
l:Left-Cerebellum-Cortex:4  
l:Left-Thalamus-Proper:5  
l:Left-Caudate:6  
l:Left-Putamen:7  
l:Left-Pallidum:8  
u:3rd-Ventricle:9  
u:4th-Ventricle:10 
u:Brain-Stem:11 
l:Left-Hippocampus:12 
l:Left-Amygdala:13 
u:CSF:14 
l:Left-Accumbens-area:15 
l:Left-VentralDC:16 
l:Left-vessel:17 
l:Left-choroid-plexus:18 
r:Right-Lateral-Ventricle:19 
r:Right-Inf-Lat-Vent:20 
r:Right-Cerebellum-White-Matter:21 
r:Right-Cerebellum-Cortex:22 
r:Right-Thalamus-Proper:23 
r:Right-Caudate:24 
r:Right-Putamen:25 
r:Right-Pallidum:26 
r:Right-Hippocampus:27 
r:Right-Amygdala:28 
r:Right-Accumbens-area:29 
r:Right-VentralDC:30 
r:Right-vessel:31 
r:Right-choroid-plexus:32 
u:5th-Ventricle:33 
u:Optic-Chiasm:34 
u:CC_Posterior:35 
u:CC_Mid_Posterior:36 
u:CC_Central:37 
u:CC_Mid_Anterior:38 
u:CC_Anterior:39 
u:ctx-lh-bankssts:40 
u:ctx-lh-caudalanteriorcingulate:41 
u:ctx-lh-caudalmiddlefrontal:42 
u:ctx-lh-cuneus:43 
u:ctx-lh-entorhinal:44 
u:ctx-lh-fusiform:45 
u:ctx-lh-inferiorparietal:46 
u:ctx-lh-inferiortemporal:47 
u:ctx-lh-isthmuscingulate:48 
u:ctx-lh-lateraloccipital:49 
u:ctx-lh-lateralorbitofrontal:50 
u:ctx-lh-lingual:51 
u:ctx-lh-medialorbitofrontal:52 
u:ctx-lh-middletemporal:53 
u:ctx-lh-parahippocampal:54 
u:ctx-lh-paracentral:55 
u:ctx-lh-parsopercularis:56 
u:ctx-lh-parsorbitalis:57 
u:ctx-lh-parstriangularis:58 
u:ctx-lh-pericalcarine:59 
u:ctx-lh-postcentral:60 
u:ctx-lh-posteriorcingulate:61 
u:ctx-lh-precentral:62 
u:ctx-lh-precuneus:63 
u:ctx-lh-rostralanteriorcingulate:64 
u:ctx-lh-rostralmiddlefrontal:65 
u:ctx-lh-superiorfrontal:66 
u:ctx-lh-superiorparietal:67 
u:ctx-lh-superiortemporal:68 
u:ctx-lh-supramarginal:69 
u:ctx-lh-frontalpole:70 
u:ctx-lh-temporalpole:71 
u:ctx-lh-transversetemporal:72 
u:ctx-lh-insula:73 
u:ctx-rh-bankssts:74 
u:ctx-rh-caudalanteriorcingulate:75 
u:ctx-rh-caudalmiddlefrontal:76 
u:ctx-rh-cuneus:77 
u:ctx-rh-entorhinal:78 
u:ctx-rh-fusiform:79 
u:ctx-rh-inferiorparietal:80 
u:ctx-rh-inferiortemporal:81 
u:ctx-rh-isthmuscingulate:82 
u:ctx-rh-lateraloccipital:83 
u:ctx-rh-lateralorbitofrontal:84 
u:ctx-rh-lingual:85 
u:ctx-rh-medialorbitofrontal:86 
u:ctx-rh-middletemporal:87 
u:ctx-rh-parahippocampal:88 
u:ctx-rh-paracentral:89 
u:ctx-rh-parsopercularis:90 
u:ctx-rh-parsorbitalis:91 
u:ctx-rh-parstriangularis:92 
u:ctx-rh-pericalcarine:93 
u:ctx-rh-postcentral:94 
u:ctx-rh-posteriorcingulate:95 
u:ctx-rh-precentral:96 
u:ctx-rh-precuneus:97 
u:ctx-rh-rostralanteriorcingulate:98 
u:ctx-rh-rostralmiddlefrontal:99 
u:ctx-rh-superiorfrontal:100
u:ctx-rh-superiorparietal:101
u:ctx-rh-superiortemporal:102
u:ctx-rh-supramarginal:103
u:ctx-rh-frontalpole:104
u:ctx-rh-temporalpole:105
u:ctx-rh-transversetemporal:106
u:ctx-rh-insula:107
----------- End regions for Haskins_Pediatric_Nonlinear_1.0 atlas --------------

2. Generate ROI masks (midACC):

Using the DD_Desai_MPM atlas, we create separate masks for the left and right midACC based on their region labels:

!whereami -mask_atlas_region DD_Desai_MPM::ctx_lh_G_and_S_cingul-Mid-Ant -prefix ./afni_pro_glm/group_results/midACC_lh_mask
!whereami -mask_atlas_region DD_Desai_MPM::ctx_rh_G_and_S_cingul-Mid-Ant -prefix ./afni_pro_glm/group_results/midACC_rh_mask

++ Input coordinates orientation set by default rules to RAI
Best match for ctx_lh_G_and_S_cingul-Mid-Ant:
   ctx_lh_G_and_S_cingul-Mid-Ant (code 7  )

** ERROR: output dataset name 'midACC_lh_mask' conflicts with existing file
** ERROR: dataset NOT written to disk!
++ Input coordinates orientation set by default rules to RAI
Best match for ctx_rh_G_and_S_cingul-Mid-Ant:
   ctx_rh_G_and_S_cingul-Mid-Ant (code 82 )

** ERROR: output dataset name 'midACC_rh_mask' conflicts with existing file
** ERROR: dataset NOT written to disk!

We then combine both hemispheres into a single bilateral ROI mask:

!3dmask_tool \
  -input ./afni_pro_glm/group_results/midACC_lh_mask+tlrc \
         ./afni_pro_glm/group_results/midACC_rh_mask+tlrc \
  -union \
  -prefix ./afni_pro_glm/group_results/midACC_mask

++ processing 2 input dataset(s), NN=2...
++ padding all datasets by 0 (for dilations)
++ frac 0 over 2 volumes gives min count 0
++ voxel limits: 0 clipped, 5546 survived, 4637855 were zero
++ writing result midACC_mask...
** ERROR: output dataset name 'midACC_mask' conflicts with existing file
** ERROR: dataset NOT written to disk!

To use the mask with Python tools like nilearn, we also convert it to NIfTI format:

! 3dAFNItoNIFTI -prefix ./afni_pro_glm/group_results/midACC_mask.nii.gz ./afni_pro_glm/group_results/midACC_mask+tlrc

++ 3dAFNItoNIFTI: AFNI version=AFNI_21.2.00 (Jul  8 2021) [64-bit]

# Load AFNI mask
roi_img = image.load_img('./afni_pro_glm/group_results/midACC_mask.nii.gz')


# Plot ROI over mni background
plotting.plot_roi(roi_img,
                  title="midACC ROI Mask",
                  display_mode='ortho',
                  cmap='autumn', draw_cross=True)

<nilearn.plotting.displays._slicers.OrthoSlicer at 0x7f2c6ef260d0>

3. Resample the Mask to Match Functional Data:

To ensure compatibility with the functional/statistical datasets, we resample the ROI mask to the same voxel resolution as the subject-level stats+tlrc files:

! 3dresample -master ./afni_pro_glm/sub-01.results/stats.sub-01+tlrc -input ./afni_pro_glm/group_results/midACC_mask+tlrc -prefix ./afni_pro_glm/group_results/midACC_rs+tlrc

** ERROR: output dataset name 'midACC_rs' conflicts with existing file
** ERROR: dataset NOT written to disk!
failure: cannot write dataset, exiting...

4. Extract Contrast Values from Each Subject:

We extract the contrast estimate for each subject by:

1. Collecting the congruent and incongruent beta sub-bricks across all subjects:

subjects = [f"sub-{i:02d}" for i in range(1, 10)]


for subj in subjects:
    stats_path = f"./afni_pro_glm/{subj}.results/stats.{subj}+tlrc"
    
    if os.path.exists(f"{stats_path}.HEAD"):  # check AFNI header file
        subprocess.run([
            "3dbucket", "-aglueto", "./afni_pro_glm/group_results/Congruent_betas+tlrc.HEAD", f"{stats_path}[1]"
        ])
        subprocess.run([
            "3dbucket", "-aglueto", "./afni_pro_glm/group_results/Incongruent_betas+tlrc.HEAD", f"{stats_path}[4]"
        ])
    else:
        print(f"Skipping {subj}: stats file not found")

++ 3dbucket: AFNI version=AFNI_21.2.00 (Jul  8 2021) [64-bit]
*+ WARNING: Over-writing dataset ././afni_pro_glm/group_results/Congruent_betas+tlrc.HEAD
++ 3dbucket: AFNI version=AFNI_21.2.00 (Jul  8 2021) [64-bit]
*+ WARNING: Over-writing dataset ././afni_pro_glm/group_results/Incongruent_betas+tlrc.HEAD
++ 3dbucket: AFNI version=AFNI_21.2.00 (Jul  8 2021) [64-bit]
*+ WARNING: Over-writing dataset ././afni_pro_glm/group_results/Congruent_betas+tlrc.HEAD
++ 3dbucket: AFNI version=AFNI_21.2.00 (Jul  8 2021) [64-bit]
*+ WARNING: Over-writing dataset ././afni_pro_glm/group_results/Incongruent_betas+tlrc.HEAD
++ 3dbucket: AFNI version=AFNI_21.2.00 (Jul  8 2021) [64-bit]
*+ WARNING: Over-writing dataset ././afni_pro_glm/group_results/Congruent_betas+tlrc.HEAD
++ 3dbucket: AFNI version=AFNI_21.2.00 (Jul  8 2021) [64-bit]
*+ WARNING: Over-writing dataset ././afni_pro_glm/group_results/Incongruent_betas+tlrc.HEAD
++ 3dbucket: AFNI version=AFNI_21.2.00 (Jul  8 2021) [64-bit]
*+ WARNING: Over-writing dataset ././afni_pro_glm/group_results/Congruent_betas+tlrc.HEAD
++ 3dbucket: AFNI version=AFNI_21.2.00 (Jul  8 2021) [64-bit]
*+ WARNING: Over-writing dataset ././afni_pro_glm/group_results/Incongruent_betas+tlrc.HEAD
++ 3dbucket: AFNI version=AFNI_21.2.00 (Jul  8 2021) [64-bit]
*+ WARNING: Over-writing dataset ././afni_pro_glm/group_results/Congruent_betas+tlrc.HEAD
++ 3dbucket: AFNI version=AFNI_21.2.00 (Jul  8 2021) [64-bit]
*+ WARNING: Over-writing dataset ././afni_pro_glm/group_results/Incongruent_betas+tlrc.HEAD
++ 3dbucket: AFNI version=AFNI_21.2.00 (Jul  8 2021) [64-bit]
*+ WARNING: Over-writing dataset ././afni_pro_glm/group_results/Congruent_betas+tlrc.HEAD
++ 3dbucket: AFNI version=AFNI_21.2.00 (Jul  8 2021) [64-bit]
*+ WARNING: Over-writing dataset ././afni_pro_glm/group_results/Incongruent_betas+tlrc.HEAD
++ 3dbucket: AFNI version=AFNI_21.2.00 (Jul  8 2021) [64-bit]
*+ WARNING: Over-writing dataset ././afni_pro_glm/group_results/Congruent_betas+tlrc.HEAD
++ 3dbucket: AFNI version=AFNI_21.2.00 (Jul  8 2021) [64-bit]
*+ WARNING: Over-writing dataset ././afni_pro_glm/group_results/Incongruent_betas+tlrc.HEAD
++ 3dbucket: AFNI version=AFNI_21.2.00 (Jul  8 2021) [64-bit]
*+ WARNING: Over-writing dataset ././afni_pro_glm/group_results/Congruent_betas+tlrc.HEAD
++ 3dbucket: AFNI version=AFNI_21.2.00 (Jul  8 2021) [64-bit]
*+ WARNING: Over-writing dataset ././afni_pro_glm/group_results/Incongruent_betas+tlrc.HEAD
++ 3dbucket: AFNI version=AFNI_21.2.00 (Jul  8 2021) [64-bit]
*+ WARNING: Over-writing dataset ././afni_pro_glm/group_results/Congruent_betas+tlrc.HEAD
++ 3dbucket: AFNI version=AFNI_21.2.00 (Jul  8 2021) [64-bit]
*+ WARNING: Over-writing dataset ././afni_pro_glm/group_results/Incongruent_betas+tlrc.HEAD

This will produce 4D images:

• Congruent_betas+tlrc → all congruent betas across subjects

• Incongruent_betas+tlrc → all incongruent betas across subjects

2. Computing the subject-wise contrast (Incongruent – Congruent) using 3dcalc:

# Create subject-wise contrast dataset (each sub-brick = Incongruent - Congruent)
! 3dcalc -a ./afni_pro_glm/group_results/Incongruent_betas+tlrc -b ./afni_pro_glm/group_results/Congruent_betas+tlrc -expr 'a-b' -prefix ./afni_pro_glm/group_results/incong_minus_cong+tlrc

++ 3dcalc: AFNI version=AFNI_21.2.00 (Jul  8 2021) [64-bit]
++ Authored by: A cast of thousands
** ERROR: output dataset name 'incong_minus_cong' conflicts with existing file
** ERROR: dataset NOT written to disk!

3. Extracting the mean contrast value within the ROI for each subject using 3dmaskave:

# Extract average contrast value from ROI for each subject
! 3dmaskave -quiet -mask ./afni_pro_glm/group_results/midACC_rs+tlrc ./afni_pro_glm/group_results/incong_minus_cong+tlrc > ./afni_pro_glm/group_results/contrast_vals.txt

++ 3dmaskave: AFNI version=AFNI_21.2.00 (Jul  8 2021) [64-bit]
+++ 207 voxels survive the mask

5. Statistical Testing: Finally, we load the contrast values and run a one-sample t-test to determine whether the average contrast across subjects significantly differs from zero:

# Load contrast values (one per subject)
contrast_vals = np.loadtxt("./afni_pro_glm/group_results/contrast_vals.txt")

# Run a one-sample t-test against 0
t_stat, p_val = ttest_1samp(contrast_vals, 0)

# Print results
print(f"Mean contrast: {np.mean(contrast_vals):.4f}")
print(f"t = {t_stat:.4f}, p = {p_val:.4f}")

Mean contrast: 0.1277
t = 2.5196, p = 0.0358

✅ Interpretation

This provides a simple but interpretable ROI-based statistical test focused on the Incongruent - Congruent contrast in the midACC. This result indicates that:

• On average, the contrast Incongruent - Congruent is positive within the mid anterior cingulate cortex (midACC) ROI.

• The difference is statistically significant at the α = 0.05 level (p = 0.036).

• This suggests that the midACC shows greater activation during Incongruent trials compared to Congruent trials across hte 9 subjects.

4.2 ROI Analysis Using a Spherical Mask

To complement the atlas-based ROI analysis, we can also define a spherical ROI centered on a coordinate of interest. This can be useful for hypothesis-driven analyses targeting specific anatomical or functional peaks.

1. Define the sphere:

• A 5mm radius sphere is created around the coordinate (0, 20, 44) using AFNI’s 3dUndump.

• The sphere is aligned to the grid of the functional data via the -master option.

echo "0 20 44" | 3dUndump -orient LPI -srad 5 -master Incongruent_betas+tlrc -prefix ConflictROI+tlrc -xyz -

# This script creates a 5mm sphere around a coordinate
# Change the x,y,z, coordinates on the left side to select a different peak
# Radius size can be changed with the -srad option

! echo "0 20 44" | 3dUndump -orient LPI -srad 5 -master ./afni_pro_glm/group_results/Incongruent_betas+tlrc -prefix ./afni_pro_glm/group_results/ConflictROI+tlrc -xyz -

++ 3dUndump: AFNI version=AFNI_21.2.00 (Jul  8 2021) [64-bit]
++ Starting to fill via -xyz coordinates
++ Total number of voxels filled = 19
** ERROR: output dataset name 'ConflictROI' conflicts with existing file
** ERROR: dataset NOT written to disk!
++ Wrote out dataset ././afni_pro_glm/group_results/ConflictROI_AA1+tlrc.BRIK

2. Extract ROI contrast values:

• The average Incongruent - Congruent contrast value will be computed for each subject using 3dmaskave:

! 3dmaskave -quiet -mask ./afni_pro_glm/group_results/ConflictROI+tlrc ./afni_pro_glm/group_results/incong_minus_cong+tlrc > ./afni_pro_glm/group_results/contrast_vals_sphere.txt

++ 3dmaskave: AFNI version=AFNI_21.2.00 (Jul  8 2021) [64-bit]
+++ 19 voxels survive the mask

3. Statistical test:

• A one-sample t-test can be performed to determine whether the contrast values within the sphere significantly differ from zero.

# Load contrast values (one per subject)
contrast_vals_sphere = np.loadtxt("./afni_pro_glm/group_results/contrast_vals_sphere.txt")

# Run a one-sample t-test against 0
t_stat_sphere, p_val_sphere = ttest_1samp(contrast_vals_sphere, 0)

# Print results
print(f"Mean contrast: {np.mean(contrast_vals_sphere):.4f}")
print(f"t = {t_stat_sphere:.4f}, p = {p_val_sphere:.4f}")

Mean contrast: 0.2919
t = 3.3636, p = 0.0099

✅ Interpretation of Sphere ROI Results

• The mean contrast value for Incongruent-Congruent in the spherical ROI is 0.2919.

• The one-sample t-test shows a significant effect at the α = 0.05 level:
  t(8) = 3.36, p = 0.0099.

• This indicates that the ROI exhibits significantly greater activation during Incongruent trials compared to Congruent trials across subjects.

Dependencies in Jupyter/Python

• Using the package watermark to document system environment and software versions used in this notebook

%load_ext watermark

%watermark
%watermark --iversions

Last updated: 2026-03-10T07:25:33.019722+00:00

Python implementation: CPython
Python version       : 3.13.11
IPython version      : 9.9.0

Compiler    : GCC 14.3.0
OS          : Linux
Release     : 5.15.0-170-generic
Machine     : x86_64
Processor   : x86_64
CPU cores   : 32
Architecture: 64bit
IPython   : 9.9.0
ipyniivue : 2.4.4
json      : 2.0.9
matplotlib: 3.10.8
nibabel   : 5.3.3
nilearn   : 0.13.1
numpy     : 2.4.2
scipy     : 1.17.0
tqdm      : 4.67.1