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/
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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/
Freesurfer mailing listFreesurfer@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.
[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.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/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/
On Tue, Jun 17, 2014 at 4:54 PM, Douglas Greve 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/
Freesurfer mailing listFreesurfer@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.
Sorry, I don't know why it is failing. We don't have a problem with it and no one else has reported this. Check the location of the FSLDIR env variable. Or maybe it is a new version of FSL that is not compatible with the old?
On 6/20/14 5:25 PM, Alan Lee wrote:
[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:
- 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 Thu, Jun 19, 2014 at 9:03 PM, Alan Lee <alan.lee@ens.fr mailto: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/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 <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> 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.
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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/
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> 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
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>
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 greve@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/
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Yes. I'm surprised that FSL would run at all without that defined. doug
On 06/23/2014 12:44 PM, Alan Lee wrote:
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/ http://sites.google.com/site/alanlflee/
On Mon, Jun 23, 2014 at 4:03 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto: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: > 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/> <http://sites.google.com/site/alanlflee/> > > > On Tue, Jun 17, 2014 at 4:54 PM, Douglas Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto: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/> >> <http://sites.google.com/site/alanlflee/> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto: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> <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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