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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