Thanks, Doug. I think I've kind of sorted that one out by creating a folder called "Retinotopy" under
freesurfer/subjects/Retinotopy/33333/, which contains the 001/, ... 004/ folders containing those their corresponding (polar and eccen) rtopy.par and f.nii files.
But now I have another problem. When I run
selxavg3-sess -a Retintopy.33333.lh -s 33333
, it runs up to the point as below, where it's "using FSL's BET to Extract Brain".
# ---------- Using FSL's BET to Extract Brain------------------ #
/usr/local/freesurfer/subjects/Retinotopy/33333/Retinotopy
bet.fsl /tmp/mkbrainmask_9112/in.nii /tmp/mkbrainmask_9112/brain -m -f 0.1
/usr/local/freesurfer//bin/bet.fsl: 1: /usr/local/freesurfer//bin/bet.fsl: /bin/remove_ext: not found
/usr/local/freesurfer//bin/bet.fsl: 1: /usr/local/freesurfer//bin/bet.fsl: /bin/remove_ext: not found
/usr/local/freesurfer//bin/bet.fsl: 1: /usr/local/freesurfer//bin/bet.fsl: /bin/imtest: not found
/usr/local/freesurfer//bin/bet.fsl: 153: [: =: unexpected operator
/usr/local/freesurfer//bin/bet.fsl: 231: /usr/local/freesurfer//bin/bet.fsl: /bin/bet2: not found
Then I realized that the program looks for those not-found files (remove_ext, imtest, bet2) in /bin/, but actually they're all in /usr/lib/fsl/5.0/.
What I did next was to copy those files from /usr/lib/fsl/5.0/ to /bin/, but then I got this error:
# ---------- Using FSL's BET to Extract Brain------------------ #
/usr/local/freesurfer/subjects/Retinotopy/33333/Retinotopy
bet.fsl /tmp/mkbrainmask_12619/in.nii /tmp/mkbrainmask_12619/brain -m -f 0.1
/bin/bet2: error while loading shared libraries: libfslvtkio.so: cannot open shared object file: No such file or directory
mri_binarize --i /tmp/mkbrainmask_12619/brain_mask.nii --min .01 --o /tmp/mkbrainmask_12619/brain_mask.nii
niiRead(): error opening file /tmp/mkbrainmask_12619/brain_mask.nii
Again, I tried copying the file libfslvtkio.so from /usr/lib/fsl/5.0 to /bin/, but it keeps giving me the same error.
So I have two questions:
1) I suspect that selxavg3-sess should be looking for the files in /usr/lib/fsl/5.0 instead of in /bin/. Why does it do that? And how can I direct it to look for files in the former location instead?
2) As a quick fix, is it OK for me to copy all the files from /usr/lib/fsl/5.0 to /bin/? Will it solve the problem? The folder /bin/ contains something else and I don't really feel like messing with it.
Many thanks,
Alan