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Nr script branch - finishing ROIs clean up #7

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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
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Binary file added ROIs_clean/MNI/coronal_plane.nii
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Binary file added ROIs_clean/MNI/csf_mask.nii.gz
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9 changes: 0 additions & 9 deletions ROIs_clean/MNI/cube01_left_mc.bdo
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9 changes: 0 additions & 9 deletions ROIs_clean/MNI/cube01_left_rcp.bdo
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9 changes: 0 additions & 9 deletions ROIs_clean/MNI/cube01_left_spinal.bdo
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9 changes: 0 additions & 9 deletions ROIs_clean/MNI/cube01_right_rcp.bdo
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9 changes: 0 additions & 9 deletions ROIs_clean/MNI/cube01_right_spinal.bdo
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9 changes: 0 additions & 9 deletions ROIs_clean/MNI/cube02_left_rcp.bdo
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9 changes: 0 additions & 9 deletions ROIs_clean/MNI/cube02_left_spinal.bdo
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9 changes: 0 additions & 9 deletions ROIs_clean/MNI/cube02_right_rcp.bdo
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9 changes: 0 additions & 9 deletions ROIs_clean/MNI/cube02_right_spinal.bdo
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9 changes: 0 additions & 9 deletions ROIs_clean/MNI/cube03_left_rcp.bdo
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9 changes: 0 additions & 9 deletions ROIs_clean/MNI/cube03_left_spinal.bdo
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9 changes: 0 additions & 9 deletions ROIs_clean/MNI/cube03_right_spinal.bdo
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9 changes: 0 additions & 9 deletions ROIs_clean/MNI/cube04_left_spinal.bdo
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9 changes: 0 additions & 9 deletions ROIs_clean/MNI/cube05_left_spinal.bdo
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9 changes: 9 additions & 0 deletions ROIs_clean/MNI/left_remaining1_box.bdo
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<?xml version="1.0" ?>
<mitkBoundingObject type="Cuboid">
<origin x="12.190488" y="32.992637" z="-28.178859" />
<WorldTransformMatrix>
<Row col1="2.500000" col2="0.000000" col3="0.000000" />
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</WorldTransformMatrix>
</mitkBoundingObject>
9 changes: 9 additions & 0 deletions ROIs_clean/MNI/left_remaining_box.bdo
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<?xml version="1.0" ?>
<mitkBoundingObject type="Cuboid">
<origin x="2.323398" y="39.881847" z="-34.219433" />
<WorldTransformMatrix>
<Row col1="2.500000" col2="0.000000" col3="0.000000" />
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<Row col1="0.000000" col2="0.000000" col3="2.500000" />
</WorldTransformMatrix>
</mitkBoundingObject>
9 changes: 9 additions & 0 deletions ROIs_clean/MNI/left_spinal_Max.bdo
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<?xml version="1.0" ?>
<mitkBoundingObject type="Cuboid">
<origin x="18.258929" y="19.252708" z="-32.501171" />
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<Row col1="2.500000" col2="0.000000" col3="0.000000" />
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<Row col1="0.000000" col2="0.000000" col3="6.940129" />
</WorldTransformMatrix>
</mitkBoundingObject>
9 changes: 9 additions & 0 deletions ROIs_clean/MNI/left_spinal_box.bdo
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<?xml version="1.0" ?>
<mitkBoundingObject type="Cuboid">
<origin x="5.526397" y="29.900560" z="-47.555739" />
<WorldTransformMatrix>
<Row col1="3.540339" col2="0.000000" col3="0.000000" />
<Row col1="0.000000" col2="3.815834" col3="0.000000" />
<Row col1="0.000000" col2="0.000000" col3="3.660886" />
</WorldTransformMatrix>
</mitkBoundingObject>
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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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<?xml version="1.0" ?>
<mitkBoundingObject type="Cuboid">
<origin x="4.775878" y="27.194829" z="-42.272441" />
<WorldTransformMatrix>
<Row col1="100.000000" col2="0.000000" col3="0.000000" />
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<Row col1="0.000000" col2="0.000000" col3="100.000000" />
</WorldTransformMatrix>
</mitkBoundingObject>
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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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<?xml version="1.0" ?>
<mitkBoundingObject type="Cuboid">
<origin x="-11.071461" y="26.370575" z="-42.369826" />
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<Row col1="2.500000" col2="0.000000" col3="0.000000" />
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<Row col1="0.000000" col2="0.000000" col3="2.500000" />
</WorldTransformMatrix>
</mitkBoundingObject>
9 changes: 9 additions & 0 deletions ROIs_clean/MNI/right_remaining_box.bdo
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<?xml version="1.0" ?>
<mitkBoundingObject type="Cuboid">
<origin x="-4.242131" y="13.099118" z="-30.331648" />
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<Row col1="5.047060" col2="0.000000" col3="0.000000" />
<Row col1="0.000000" col2="2.893964" col3="0.000000" />
<Row col1="0.000000" col2="0.000000" col3="2.951412" />
</WorldTransformMatrix>
</mitkBoundingObject>
9 changes: 9 additions & 0 deletions ROIs_clean/MNI/right_spinal10.bdo
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<?xml version="1.0" ?>
<mitkBoundingObject type="Cuboid">
<origin x="-14.739682" y="45.601696" z="-62.712983" />
<WorldTransformMatrix>
<Row col1="4.200070" col2="0.000000" col3="0.000000" />
<Row col1="0.000000" col2="-6.585730" col3="0.000000" />
<Row col1="0.000000" col2="0.000000" col3="7.699248" />
</WorldTransformMatrix>
</mitkBoundingObject>
9 changes: 9 additions & 0 deletions ROIs_clean/MNI/right_spinal11.bdo
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<?xml version="1.0" ?>
<mitkBoundingObject type="Cuboid">
<origin x="-20.581452" y="28.819889" z="-49.215421" />
<WorldTransformMatrix>
<Row col1="7.075788" col2="0.000000" col3="0.000000" />
<Row col1="0.000000" col2="5.145319" col3="0.000000" />
<Row col1="0.000000" col2="0.000000" col3="7.732256" />
</WorldTransformMatrix>
</mitkBoundingObject>
9 changes: 9 additions & 0 deletions ROIs_clean/MNI/right_spinal12.bdo
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<?xml version="1.0" ?>
<mitkBoundingObject type="Cuboid">
<origin x="0.946113" y="49.705677" z="-65.219125" />
<WorldTransformMatrix>
<Row col1="0.795250" col2="0.000000" col3="0.000000" />
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<Row col1="0.000000" col2="0.000000" col3="3.822362" />
</WorldTransformMatrix>
</mitkBoundingObject>
9 changes: 9 additions & 0 deletions ROIs_clean/MNI/right_spinal_box.bdo
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<?xml version="1.0" ?>
<mitkBoundingObject type="Cuboid">
<origin x="-8.132759" y="29.141201" z="-45.088057" />
<WorldTransformMatrix>
<Row col1="3.521607" col2="0.000000" col3="0.000000" />
<Row col1="0.000000" col2="3.214221" col3="0.000000" />
<Row col1="0.000000" col2="0.000000" col3="3.621745" />
</WorldTransformMatrix>
</mitkBoundingObject>
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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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9 changes: 0 additions & 9 deletions ROIs_clean/MNI/sphere01_left_mc.bdo
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9 changes: 0 additions & 9 deletions ROIs_clean/MNI/sphere01_left_spinal.bdo
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9 changes: 0 additions & 9 deletions ROIs_clean/MNI/sphere02_left_mc.bdo
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