Hi again Josselin,
> -so my template_list file is in my fslvbm directory (I also
> put a copy of it
> in my struc directory). Here is its contents (all on the
> same line):
> con_01.nii con_02.nii con_03.nii con_04.nii con_05.nii
> con_06.nii con_07.nii
> con_08.nii con_09.nii con_10.nii con_11.nii con_13.nii
> con_14.nii \
> pat_004.nii pat_007.nii pat_012.nii pat_013.nii pat_002.nii
> pat_022.nii
> pat_034.nii pat_061.nii pat_021.nii pat_018.nii pat_009.nii
> pat_041.nii
> pat_006.nii
For some reasons (it's working for me here), the \ is not taken into account properly when you're running fslvbm2c on your system. Susbequently, it tries to find a "\struc_GM_to_T" that obviously does not exist.
The easiest way is to copy all the names of the scans in a single column in your template_list file, which only needs to be in your fslvbm/ directory, and this should work fine.
You can check this by just typing in your struc/ directory:
template_check=`cat ../template_list`
template_check=`$FSLDIR/bin/remove_ext $template_check`
for g in $template_check ; do
mergecheck="$mergecheck ${g}_struc_GM_to_T"
done
in a shell and look at the output of:
echo $mergecheck
Cheers,
Gwenaelle
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