Hi,
I am running the script run_first_all on my T1 images. This script does not always generates the all_fast_firstseg.nii.gz file, which I need to do the volumetric analysis of subcortical structures. It does generate all the other .vtk, bvars, and .com files.
Ant ideas why this happens?
Also, can I use the .vtk file to get the volume info?
for example: first_utils --meshToVol -m mesh.vtk -i t1_image.nii.gz -l fill_value -o output_name
and then get the volume by:
fslstats output_name -l 16.5 -u 17.5 -V ?
I tried volume analysis using both .vtk and all_fast_firstseg.nii.gz files on one of the subjects, but these two methods five different results. not sure why this ocurs?
Any ideas?
Tx so much for your help,
aj
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