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.com<mailto:cgxz...@gmail.com>
> > zho...@livemail.uthscsa.edu<mailto: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