Hello,
I'm trying to run FIRST to segment subcortical regions (caudate, putamen, globus pallidus). I've been running the following command:
run_first_all -i sub-001 -o sub-001 -s L_Caud,L_Puta,L_Pall
Then to get their volumetric data:
fslstats sub-001-L_Caud_corr.nii.gz -l 10.5 -u 11.5 -V
fslstats sub-001-L_Puta_corr.nii.gz -l 11.5 -u 12.5 -V
fslstats sub-001-L_Pall_corr.nii.gz -l 12.5 -u 13.5 -V
Unfortunately I seem to be getting very small output volumes. For example, for the putamen, the volume is said to be 924. I also opened the binary files and it seems very small compared to the original input file. Any suggestions or comments would be greatly appreciated!
Thank you.
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