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nasrin100 wants to merge 49 commits into from
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Nr script branch #1

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d3d9ab8
add 3x3 grid + merged output in trigeminal pipeline
nasrin100 Oct 29, 2025
d738046
add 3x3 grid + merged output in trigeminal pipeline
nasrin100 Oct 29, 2025
504d4f5
Update trigeminal_first_order_nr.sh
nasrin100 Nov 3, 2025
599c03a
Update trigeminal_first_order_nr.sh
nasrin100 Nov 11, 2025
59f1583
Update trigeminal_first_order_nr.sh
nasrin100 Nov 11, 2025
1749142
clean code - arnaud with nasrin
nasrin100 Nov 11, 2025
dbf8e5e
change permission
nasrin100 Nov 11, 2025
cfdf0c0
fix git tree
nasrin100 Nov 11, 2025
e013eee
just for test i added #before 0.2
nasrin100 Nov 11, 2025
034c947
removed the loop for subjects
nasrin100 Nov 11, 2025
42cdff5
s removed from subjects
nasrin100 Nov 13, 2025
6633786
comment added for -m
nasrin100 Nov 13, 2025
34ec346
comment on specific step size and theta
nasrin100 Nov 13, 2025
3310f2b
all the comments + concatenation step moved before registration
nasrin100 Nov 18, 2025
3bf7cae
Clarify npv seeding comment, Add 3 subfolders for segmentation, Remov…
nasrin100 Nov 20, 2025
a04dfc9
did all the comments
nasrin100 Nov 27, 2025
572a9da
merge main
nasrin100 Nov 27, 2025
b2a2f2b
Merge branch 'main' into nr_script_branch
nasrin100 Nov 27, 2025
af1fb9f
inverse is used for bringing mni to orig in step 9
nasrin100 Dec 3, 2025
548011d
Add new ROI files in ROIs_clean/MNI
nasrin100 Dec 4, 2025
86e6ba8
Add new ROI files in ROIs_clean/MNI
nasrin100 Dec 5, 2025
0112afc
rois in right_spinal
nasrin100 Dec 11, 2025
fcc8995
new rois
nasrin100 Dec 11, 2025
735d31d
applying new rois after checking all tracts of 40 subjects
nasrin100 Dec 11, 2025
dd4e880
Add new ROI files in ROIs_clean/MNI
nasrin100 Dec 11, 2025
d270577
new roi added after second runnig of all subjects
nasrin100 Dec 12, 2025
bcc813f
Add new ROI files in ROIs_clean/MNI
nasrin100 Dec 12, 2025
e7ccab1
Add new ROI files in ROIs_clean/MNI
nasrin100 Dec 12, 2025
8bee7ca
Add new ROI files in ROIs_clean/MNI
nasrin100 Jan 5, 2026
6042231
Add new ROI files in ROIs_clean/MNI
nasrin100 Jan 6, 2026
93b90fe
Add new ROI files in ROIs_clean/MNI
nasrin100 Jan 14, 2026
61640cc
Add new ROI files in ROIs_clean/MNI
nasrin100 Jan 15, 2026
756bb74
right_left spinal added for right side
nasrin100 Jan 15, 2026
c213567
Add new ROI files in ROIs_clean/MNI
nasrin100 Jan 16, 2026
b77ee1b
added new_coronal and new_lower
nasrin100 Jan 19, 2026
0f60de5
Add new plane files in ROIs_clean/MNI
nasrin100 Jan 19, 2026
fad7934
Remove unused BDO ROIs from MNI folder
nasrin100 Jan 21, 2026
bed6e1c
Add CSF in ROIs_clean/MNI
nasrin100 Jan 23, 2026
b87ee6a
added new_lower for cleaning spinal
nasrin100 Feb 2, 2026
c591b89
Add new_lower in ROIs_clean/MNI
nasrin100 Feb 2, 2026
269a474
Add new_lower in ROIs_clean/MNI
nasrin100 Feb 2, 2026
798ba78
Add new_lower in ROIs_clean/MNI
nasrin100 Feb 2, 2026
bab104c
Add deviated_br for spinal in ROIs_clean/MNI
nasrin100 Feb 16, 2026
5faf39d
Add deviated_br for spinal in ROIs_clean/MNI
nasrin100 Feb 23, 2026
2d18c2b
update
nasrin100 Feb 27, 2026
247fa94
Remove accidentally committed scripts
nasrin100 Feb 27, 2026
876d00c
Remove accidentally committed scripts
nasrin100 Feb 27, 2026
092b724
Remove accidentally committed scripts
nasrin100 Feb 27, 2026
c4318b6
update
nasrin100 Feb 27, 2026
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9 changes: 9 additions & 0 deletions ROIs_clean/MNI/Selection Cube 02.bdo
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9 changes: 9 additions & 0 deletions ROIs_clean/MNI/left_remaining1_box.bdo
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9 changes: 9 additions & 0 deletions ROIs_clean/MNI/left_remaining_box.bdo
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9 changes: 9 additions & 0 deletions ROIs_clean/MNI/left_spinal_Max.bdo
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9 changes: 9 additions & 0 deletions ROIs_clean/MNI/left_spinal_box.bdo
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9 changes: 9 additions & 0 deletions ROIs_clean/MNI/left_spinal_deviation.bdo
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Binary file added ROIs_clean/MNI/left_spinal_deviation.nii.gz
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9 changes: 9 additions & 0 deletions ROIs_clean/MNI/left_spinal_neck.bdo
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Binary file added ROIs_clean/MNI/left_thalamus_231_245_brainnetome.nii.gz
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Binary file added ROIs_clean/MNI/left_thalamus_231_245_brainnetome__to_mni_masked.nii.gz
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Binary file added ROIs_clean/MNI/mni_masked.nii
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9 changes: 9 additions & 0 deletions ROIs_clean/MNI/new_coronal.bdo
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Binary file added ROIs_clean/MNI/new_lower.nii.gz
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9 changes: 9 additions & 0 deletions ROIs_clean/MNI/pontomedullar.bdo
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9 changes: 9 additions & 0 deletions ROIs_clean/MNI/right_remaining_box.bdo
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9 changes: 9 additions & 0 deletions ROIs_clean/MNI/right_spinal10.bdo
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9 changes: 9 additions & 0 deletions ROIs_clean/MNI/right_spinal11.bdo
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9 changes: 9 additions & 0 deletions ROIs_clean/MNI/right_spinal12.bdo
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9 changes: 9 additions & 0 deletions ROIs_clean/MNI/right_spinal_box.bdo
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9 changes: 9 additions & 0 deletions ROIs_clean/MNI/right_spinal_deviation.bdo
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Binary file added ROIs_clean/MNI/right_thalamus_232_246_brainnetome.nii.gz
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Binary file added ROIs_clean/MNI/right_thalamus_232_246_brainnetome__to_mni_masked.nii.gz
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