Hi Sahar,
Thanks for that. With the script below, it seems to loop through the images but produces no outputs and I'm still getting this error message:
fslmaths temp_FAt3_?_tfce_thr0point95.nii.gz -mas PostThalamicRadLeft.nii.gz temp_FAt3_?_tfce_thr0point95_PostThalamicRadLeft
Error in command line: unknown option "temp_FAt3_2_tfce_thr0point95.nii.gz"
Again, I really appreciate your help with this.
Meg
Hi Meghan,
My mistake ,sorry.
Instead of fslmath type falmaths.
#!/bin/bash
for N in $(cat mask)
do
BASE=$(echo $N | sed 's/.\{7\}$//g')
echo "fslmaths temp_FAt3_?_tfce_thr0point95.nii.gz -mas $N temp_FAt3_?_tfce_thr0point95_${BASE}"
fslmaths temp_FAt3_?_tfce_thr0point95.nii.gz -mas $N temp_FAt3_?_tfce_thr0point95_${BASE}
done
echo will print the line in advance and will help you to trigger the error.
Regards
Sahar
On Sat, Oct 5, 2013 at 7:55 PM, Meghan McIlwain <[log in to unmask]> wrote:
Thanks, Sahar. I think it's almost there... Here's the error message I get now:
Error in command line: unknown option "temp_FAt3_2_tfce_thr0point95.nii.gz"
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