Hi Doug,
I think I didnt explain clearly last time.
Here's the thing:
I have four runs: 2 eccen and 2 polars. I followed the process http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis and I hope to view the result of an individual session, e.g. one polar, which could display the activations with different angles. What should I do after all the analysis is done? Or I should run a retinotopy analysis different from the link above.
Thank you in advance.
Best
Wei
----
Hi Wei, do you have both polar and eccentricity? It looks like you only have polar. doug
On 11/19/2012 01:39 PM, Zhou, Wei wrote: > Please find the Xtmp.mat in the attachment.Thank you, Doug. > Best > Wei > ---- > 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 > > Best > Wei Zhou > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer