[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/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/ On Thu, Jun 19, 2014 at 9:03 PM, Alan Lee <alan....@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/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/ > > > On Tue, Jun 17, 2014 at 4:54 PM, Douglas Greve <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/ >> >> >> _______________________________________________ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> 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. >> >> >
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