Can you send the full terminal output? doug On 11/27/2012 05:55 PM, Zhou, Wei wrote:
Hi Doug, Thank you for reply. yes all 4 are in bold separately. I tried -run-wise with selxavg3-sess, but it failed with the following msg: Saving X matrix to /media/local_home/zhouw4/EM0220/analysis/retinotopy/SUBJ01/bold/rtopy.self.lh/pr001/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 attach the mat file in the email. I am thinking that the error is similar as that I only put polar or eccen session in bold folder. Thank you for looking into it. Best Wei ________________ But all four runs into a single bold folder, then try running selxavg3-sess with the -run-wise option. This will create separate run analysis in the output directory. I have not tried it with retinotopy before, so get back to me if it fails. doug On 11/26/2012 05:53 PM, Zhou, Wei wrote:
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 processhttp://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 exportingSUBJECTS_DIR to
the
directory of upper fold, retinotopy or SUBJ01 But none ofthem
works.
Still the same error msg. So what should SUBJECTS_DIR be exported to for thisanalysis?
Best Wei >Hi Wei, this is a bug in the error msg. It is trying tosay 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 someidea 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.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.eduhttps://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