Hi Doug,
The subject name for structural is "SUBJ1" when I did recon-all, which is also the content of file "subjectname". My dir structures of "structural" and "retinotopy" are the same as http://www.alivelearn.net/?p=65 . "SUBJ1" is stored under "structural". if I set SUBJECTS_DIR as "....../structural", $SUBJECT_DIR/SUBJ1 does exist, then still I get the same error msg.
The following is the log file:
fieldsign-sess log file $Id: fieldsign-sess,v 1.2 2010/05/04 22:00:18 greve Exp $ Thu Nov 1 10:36:52 CDT 2012 Linux rii-appserv-02 2.6.32-279.11.1.el6.x86_64 #1 SMP Sat Sep 22 07:10:26 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux /media/users/zhouw4/testf/retinotopy /usr/local/freesurfer/fsfast/bin/fieldsign-sess -a rtopy.self.lh -occip -s SUBJ1 uid=20120(zhouw4) gid=22000(rii_users) groups=22000(rii_users),21100(rii_appservers),23000(domain^users) context=unconfined_u:unconfined_r:unconfined_t:s0-s0:c0.c1023
Best Wei
What is the name of FreeSurfer subject? This is not necessarily the same >> as SUBJ01 in your command line below. That is the session (which may or may not be the same as the "subject name"). What ever the subjectname is, does SUBJECT_DIR/subject exist?
On 10/31/2012 03:07 PM, Zhou, Wei wrote:
Hi, Doug
Thank you for your reply. I have tried exporting SUBJECTS_DIR to the directory of upper fold, retinotopy or SUBJ01 But none of them works. Still the same error msg.
So what should SUBJECTS_DIR be exported to for this analysis?
Best
Wei
Hi Wei, this is a bug in the error msg. It is trying to say that your source subject is not in the $SUBJECTS_DIR. doug
On 10/27/2012 02:27 PM, Zhou, Wei wrote: Dear freesurfers,
I am trying retinotopy analysis in freesurfer. For "fieldsign-sess", I encounter the following problem when I type "fieldsign-sess -a rtopy.self.lh -occip -s SUBJ01" or "fieldsign-sess -a rtopy.self.lh -occip -sf sessid":
*/media/users/zhouw4/testf/retinotopy/SUBJ01/log/fieldsign-sess.log* *subject: Undefined variable.*
my structure of retinotopy fold is : retinotopy | |--sessid |--SUBJ01 |--subjectname
|--bold |--001 |--f.nii |--rtopy.par|I really appreciate it if you could give me some idea about that problem. Thanks a lot in advance.
Best Wei Zhou Medical Physics Ph.D. Student Diagnostic Imaging Track cgxz...@gmail.commailto:cgxz...@gmail.com zho...@livemail.uthscsa.edumailto:zho...@livemail.uthscsa.edu
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Best Wei Zhou Medical Physics Ph.D. Student cgxzwwd@gmail.commailto:cgxzwwd@gmail.com zhouw4@livemail.uthscsa.edumailto:zhouw4@livemail.uthscsa.edu
Try using this version
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fieldsign-sess
doug
On 11/01/2012 11:47 AM, Zhou, Wei wrote:
Hi Doug,
The subject name for structural is "SUBJ1" when I did recon-all, which is also the content of file "subjectname". My dir structures of "structural" and "retinotopy" are the same as http://www.alivelearn.net/?p=65 . "SUBJ1" is stored under "structural". if I set SUBJECTS_DIR as "....../structural", $SUBJECT_DIR/SUBJ1 does exist, then still I get the same error msg.
The following is the log file:
fieldsign-sess log file $Id: fieldsign-sess,v 1.2 2010/05/04 22:00:18 greve Exp $ Thu Nov 1 10:36:52 CDT 2012 Linux rii-appserv-02 2.6.32-279.11.1.el6.x86_64 #1 SMP Sat Sep 22 07:10:26 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux /media/users/zhouw4/testf/retinotopy /usr/local/freesurfer/fsfast/bin/fieldsign-sess -a rtopy.self.lh -occip -s SUBJ1 uid=20120(zhouw4) gid=22000(rii_users) groups=22000(rii_users),21100(rii_appservers),23000(domain^users) context=unconfined_u:unconfined_r:unconfined_t:s0-s0:c0.c1023
Best Wei
What is the name of FreeSurfer subject? This is not necessarily the
same >>
as SUBJ01 in your command line below. That is the session (which may or may not be the same as the "subject name"). What ever the subjectname
is, does SUBJECT_DIR/subject exist? On 10/31/2012 03:07 PM, Zhou, Wei wrote:
Hi, Doug
Thank you for your reply. I have tried exporting SUBJECTS_DIR to the directory of upper fold, retinotopy or SUBJ01 But none of them works. Still the same error msg.
So what should SUBJECTS_DIR be exported to for this analysis?
Best
Wei
Hi Wei, this is a bug in the error msg. It is trying to say that your source subject is not in the $SUBJECTS_DIR. doug
On 10/27/2012 02:27 PM, Zhou, Wei wrote: Dear freesurfers,
I am trying retinotopy analysis in freesurfer. For "fieldsign-sess", I encounter the following problem when I type "fieldsign-sess -a rtopy.self.lh -occip -s SUBJ01" or "fieldsign-sess -a rtopy.self.lh -occip -sf sessid":
*/media/users/zhouw4/testf/retinotopy/SUBJ01/log/fieldsign-sess.log* *subject: Undefined variable.*
my structure of retinotopy fold is : retinotopy | |--sessid |--SUBJ01 |--subjectname
|--bold |--001 |--f.nii |--rtopy.par|I really appreciate it if you could give me some idea about that problem. Thanks a lot in advance.
Best Wei Zhou Medical Physics Ph.D. Student Diagnostic Imaging Track cgxz...@gmail.commailto:cgxz...@gmail.com zho...@livemail.uthscsa.edumailto:zho...@livemail.uthscsa.edu
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Best Wei Zhou Medical Physics Ph.D. Student cgxzwwd@gmail.com mailto:cgxzwwd@gmail.com zhouw4@livemail.uthscsa.edu mailto:zhouw4@livemail.uthscsa.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Zhou, Wei