You should have all of your run folders under bold. It looks like you have only 001 under bold. doug
On 11/24/2012 12:07 PM, Zhou, Wei wrote:
Hi Doug,
Thank you for reply. As in rtopy.par the stimtype is either polar or eccen, I get separate f.nii files for eccen and polar and do one of the two at one time. Do you mean I should combine polar and eccen sessions into one f.nii? e.g. i want to do polar analysis whose rtopy.par file is polar, but I still need to put eccen session into f.nii with polar and then do the analysis?
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 tothe
directory of upper fold, retinotopy or SUBJ01 But none of themworks.
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 thatyour
>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 -artopy.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 aboutthat
> 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.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/freesurferBest Wei Zhou Medical Physics Ph.D. Student 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
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
-- 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