Did you run fieldsign-sess? If you don't have an eccen run you can't compute a fieldsign. doug ps. Please post emails to the list and not to me personally. Thanks!
On 03/27/2012 04:07 PM, Kiley Seymour wrote:
Dear Doug,
Thanks for all of your help today. I think I am almost there with this retinotopy analysis. But the error below has halted me. I have fieldsign folder, but only a fsig.nii.gz exists (i.e. no fieldsign file) though.
% tksurfer-sess -a rtopy.self.lh -s IFEE2211 -fieldsign Surface self lh Map Surface self lh $Id: tksurfer-sess,v 1.16.2.1 2011/04/05 22:25:15 greve Exp $ Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux Tue Mar 27 15:46:22 EDT 2012 /home/virtualuser/freesurfer/tktools/tksurfer
list fieldsign ERROR: could not determine file for /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/rtopy.self.lh/fieldsign/fieldsign child process exited abnormally
On Tue, Mar 27, 2012 at 7:28 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
You will have to mri_convert all the .nii files so that they have the proper TR.
On 03/27/2012 12:51 PM, Kiley Seymour wrote:
Hi Doug. I just made a dummy folder with an eccen run. It got around the error XCond = cond(XtX) but took me back to the original error : TR mismatch error despite me re-doing the preprocessing and re- mri_concat-enating my SPM nii files into a 4D file for each run.
Do you think using mri_concat with --regheader could be the problem? Or perhaps the fact that dicoms were converted to nii files in a program that was not freesufer?
K
On Tue, Mar 27, 2012 at 6:35 PM, Kiley Seymour kileyseymour@googlemail.com wrote:
no I don't.
On Tue, Mar 27, 2012 at 6:17 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Do you not have any eccen runs? doug
On 03/27/2012 06:55 AM, Kiley Seymour wrote:
Dear Doug,
I am aware I am becoming a regular pain. But I now encounter the following problem when running selxavg3-sess -a rtopy.self.lh -s CMRU1711. I have also attached my analysis.info and Xtmp.mat files
Thanks for all of your suggestions.
K
#@# CMRU1711 ############################### /media/sf_DATA1/RETINOTOPY/CMRU1711
$Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ /home/virtualuser/freesurfer/fsfast/toolbox/fast_selxavg3.m /home/virtualuser/freesurfer/fsfast/toolbox/fast_ldanaflac.m /home/virtualuser/freesurfer/matlab/MRIread.m
outtop = /media/sf_DATA1/RETINOTOPY Extension format = nii.gz nruns = 3 autostimdur =
outanadir = /media/sf_DATA1/RETINOTOPY/CMRU1711/bold/rtopy.self.lh Found 138599/149490 (92.7) voxels in mask Creating Design Matrix ... creation time = 0.008 sec DoMCFit = 1 ntptot = 369, nX = 33, DOF = 336 Saving X matrix to /media/sf_DATA1/RETINOTOPY/CMRU1711/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);
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Douglas N Greve