It looks like label 7 was not in the volume. Where did aparc+aseg.nii come from?
On 8/26/2021 1:37 PM, A.R. Sekar wrote:
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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
sysnameDarwin
hostname CIDDRGs-MacBook-Air.local
machinex86_64
user ciddrg
inputaparc+aseg.nii.gz
frame0
nErode3d 0
nErode2d 0
output aparc+aseg_labels_label7.mgz
Binarizing based on matching values
nMatch 1
0 7
binval1
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
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