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 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 -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/freesurfer
Best 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