Please find the Xtmp.mat in the attachment.Thank you, Doug.
Best
Wei
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Can you send me the Xtmp.mat file? dloug On 11/16/2012 01:01 PM, Zhou, Wei wrote: > 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> > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > Best > Wei Zhou > > > > _______________________________________________ > 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