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 > <kileyseym...@googlemail.com> wrote: >> no I don't. >> >> On Tue, Mar 27, 2012 at 6:17 PM, Douglas N Greve >> <gr...@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); >>>> >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is intended only for the person to whom it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
