Yes, I've installed FSL already. I can launch FSL by typing "fslview" in the command window.
However, it seems that the $FSLDIR is not defined. Should I define it manually using setenv before running selxavg3-sess?
-- Alan Lee sites.google.com/site/alanlflee/
On Mon, Jun 23, 2014 at 4:03 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Do you have FSL installed? If so, what is your $FSLDIR?
On 06/19/2014 03:03 PM, Alan Lee 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/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:
- 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
-- Alan Lee sites.google.com/site/alanlflee/ <
http://sites.google.com/site/alanlflee/%3E
On Tue, Jun 17, 2014 at 4:54 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
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 33333 Surface 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 $ root setenv FREESURFER_HOME /usr/local/freesurfer/ setenv SUBJECTS_DIR /usr/local/freesurfer/subjects/Structural Linux 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 -nolog Tue Jun 17 15:44:05 CEST 2014 instem f mc 1 f fmcpr stc 0 fmcpr sm 0 mask 1 brain 33333 Template ----------------------------- mktemplate-sess -s 33333 -d /usr/local/freesurfer/subjects/Retinotopy -fsd Retinotopy -nolog -update Session: /usr/local/freesurfer/subjects/Retinotopy/33333 ---------------- Tue Jun 17 15:44:06 CEST 2014 ERROR: /usr/local/freesurfer/subjects/Retinotopy/33333/Retinotopy does not exist ===================== -- Alan Lee sites.google.com/site/alanlflee/ <http://sites.google.com/site/alanlflee/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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