Hello Experts,

 

Hope you are well! I am trying to extract ROIs from the aparc+aseg file after running recon all however, I am getting the following result for all my images:

 

ciddrg@CIDDRGs-MacBook-Air C961060 % cd /Volumes/Akila/Cambridge/C961022 

ciddrg@CIDDRGs-MacBook-Air C961022 % isolate_labels.csh --vol aparc+aseg.nii --outprefix aparc+aseg_labels --L $label 7

Input file: aparc+aseg.nii

Output prefix: aparc+aseg_labels

mri_convert aparc+aseg.nii aparc+aseg.nii.gz 

reading from aparc+aseg.nii...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to aparc+aseg.nii.gz...

Label of interest: 7

Number of voxels and volume for label 7 is = (0, 0.000000mm^3)

mri_binarize --i aparc+aseg.nii.gz --match 7 --o aparc+aseg_labels_label7.mgz

 

7.1.1

cwd /Volumes/Akila/Cambridge/C961022

cmdline mri_binarize --i aparc+aseg.nii.gz --match 7 --o aparc+aseg_labels_label7.mgz 

sysname  Darwin

hostname CIDDRGs-MacBook-Air.local

machine  x86_64

user     ciddrg

 

input      aparc+aseg.nii.gz

frame      0

nErode3d   0

nErode2d   0

output     aparc+aseg_labels_label7.mgz

Binarizing based on matching values

nMatch 1

 0     7

binval        1

binvalnot     0

fstart = 0, fend = 0, nframes = 1

Found 0 values in range

Counting number of voxels in first frame

Found -1 voxels in final mask

Count: -1 -1.000000 16777216 -0.000006

mri_binarize done

ciddrg@CIDDRGs-MacBook-Air C961022 % 

 

Could you help me with where the error might be? I would really appreciate your help, thank you!

 

Regards,

Akila