My name is John Hegarty, and I have been pleased to utilize FSL for a
volumetric MRI study I am conducting. I am relatively new to FSL and
unix coding alike. I am simply attempting to output the information
from FAST to obtain a voxel number of CSF, GM, and WM. When I run the
coding from the example script on the site I get an error message from
each step of the script. I don't really care if I have to multiply the
numbers by hand because the variables aren't working, but I want to be
sure that the vol and mean values are correct and that I can utilize
these for my analyses. I was wondering if there were a way for me to
verify that I am getting the correct output from my files. I
appreciate your help. I have attached my code and error messages below.
Regards,
John Hegarty
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#!/bin/csh
foreach Subjects (AB)
cd /applications/neuroimaging/olfact_mem/scans/delineate/nifti
vol=`$FSLDIR/bin/fslstats COPY_${Subjects}_struc_Resize_brain_susan_pve_0
-V | awk '{print $1}'`
mean=`$FSLDIR/bin/fslstats COPY_$
{Subjects}_struc_Resize_brain_susan_pve_0 -M`
tissuevol=`echo "$mean * $vol" | bc -1`
echo $tissuevol
end
vol=150122: Command not found.
mean=0.773635: Command not found.
mean: Undefined variable.
tissuevol=: Command not found.
tissuevol: Undefined variable.
--
John Hegarty
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Lifespan Human Senses Lab
San Diego State University
619-594-3733
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