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 <gr...@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: > > 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 > > > > > > > > > > > > -- > > Alan Lee > > sites.google.com/site/alanlflee/ < > http://sites.google.com/site/alanlflee/> > > > > > > On Tue, Jun 17, 2014 at 4:54 PM, Douglas Greve > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@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> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto: > Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended only for the person to > > whom it is > > addressed. If you believe this e-mail was sent to you in error and > > the e-mail > > contains patient information, please contact the Partners > > Compliance HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to > > you in error > > but does not contain patient information, please contact the > > sender and properly > > dispose of the e-mail. > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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