Hi Doug,
It seems the previous fieldsign-sess problem is due to that I stored data on one server while freesurfer is on the other server.
But when I put the data and freesurfer on the same server and run the retinotopy analysis again, it reported fail msg for "selxavg3-ses" :
--
ntptot = 80, nX = 27, DOF = 53
Saving X matrix to /media/local_home/zhouw4/testf/retinotopy/SUBJ01/bold/rtopy.self.lh/Xtmp.mat
Error using svd
Input to SVD must not contain NaN or Inf.
Error in cond (line 39)
s = svd(A);
Error in fast_selxavg3 (line 254)
XCond = cond(XtX);
---
I checked Xtmp.mat. There is NaN in Xn and XtX.
My rtopy par is: eccen and pos.
Would you please give me some idea about this error?
Best
Wei
>>
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.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
> cgxz...@gmail.com <mailto:cgxz...@gmail.com>
> zho...@livemail.uthscsa.edu <mailto:zho...@livemail.uthscsa.edu>
>
>
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