[sorry, I may have sent this multiple times, but, because I'm not sure if it got through because I got several "bounce-back" error messages, I'm sending it out again...]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/Retinotopybet.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/Retinotopybet.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 directorymri_binarize --i /tmp/mkbrainmask_12619/brain_mask.nii --min .01 --o /tmp/mkbrainmask_12619/brain_mask.niiniiRead(): 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
On Thu, Jun 19, 2014 at 9:03 PM, Alan Lee <alan.lee@ens.fr> wrote:
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/Retinotopybet.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/Retinotopybet.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 directorymri_binarize --i /tmp/mkbrainmask_12619/brain_mask.nii --min .01 --o /tmp/mkbrainmask_12619/brain_mask.niiniiRead(): 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
On Tue, Jun 17, 2014 at 4:54 PM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:
The information in this e-mail is intended only for the person to whom it is
It looks for it in the current folder. You must run this from the same folder you ran mkanalysis-sess from (which should be your project folder)
On 6/17/14 4:13 PM, Alan Lee wrote:
Hello,
I'm using freesurfer to do retinotopic mapping. I've completed the recon-all, mkanalysis-sess, mri-convert and preproc-sess steps. Now when I run the selxavg3-sess (my subject name is 33333):
selxavg3-sess -a Retinotopy.33333.lh -s 33333
I got the following message:"ERROR: /usr/local/freesurfer/subjects/Retinotopy/33333/Retinotopy does not exist"
It seems to look for a Retintopy folder within /Retinotopy/33333/. I suppose the Retinotopy folder should be placed under freesurfer/subjects/ ? Am I missing something here?
Any help would be greatly appreciated.
Many thanks,Alan
=====================debian:/usr/local/freesurfer/subjects/Retinotopy# selxavg3-sess -a Retinotopy.33333.lh -s 33333Surface data self lh--------------------------------------------------------------selxavg3-sess logfile is /usr/local/freesurfer/subjects/Retinotopy/log/selxavg3-sess-Retinotopy-Retinotopy.33333.lh-140617154401.log--------------------------------------------------------------preproc-sess -s 33333 -d /usr/local/freesurfer/subjects/Retinotopy -a Retinotopy.33333.lh -nolog--------------------------------------------------------------preproc-sess logfile is /dev/null--------------------------------------------------------------$Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $rootsetenv FREESURFER_HOME /usr/local/freesurfer/setenv SUBJECTS_DIR /usr/local/freesurfer/subjects/StructuralLinux debian 3.2.0-4-486 #1 Debian 3.2.57-3+deb7u1 i686 GNU/Linux/usr/local/freesurfer/subjects/Retinotopy/usr/local/freesurfer//fsfast/bin/preproc-sess-s 33333 -d /usr/local/freesurfer/subjects/Retinotopy -a Retinotopy.33333.lh -nologTue Jun 17 15:44:05 CEST 2014instem fmc 1 f fmcprstc 0 fmcprsm 0mask 1 brain33333 Template -----------------------------mktemplate-sess -s 33333 -d /usr/local/freesurfer/subjects/Retinotopy -fsd Retinotopy -nolog -updateSession: /usr/local/freesurfer/subjects/Retinotopy/33333 ----------------Tue Jun 17 15:44:06 CEST 2014ERROR: /usr/local/freesurfer/subjects/Retinotopy/33333/Retinotopy does not exist
=====================
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