You'll have to re-run the preprocessing (or change all the .nii files). doug
Kiley Seymour wrote: > Dear Doug, > > Thanks for your earlier reply. I have installed fsl on my machine, and > have progressed a little further through the retinotopy analysis. > However, I now have the following error. > > ERROR: TR mismatch between analysis and data > analysis TR = 2, data TR = 0 > > I used > > mri_convert f.nii f.nii -tr 2000 > > to try to fix the problem, but had no success (below is the output). > > Your help would be very much appreciated. > > Thanks in advance > > Kiley > > > FreeSurfer:/data1/RETINOTOPY> selxavg3-sess -a rtopy.self.lh -s > IFEE2211 -no-preproc > Surface data self lh > -------------------------------------------------------------- > selxavg3-sess logfile is > /media/sf_DATA1/RETINOTOPY/log/selxavg3-sess-bold-rtopy.self.lh-120326071335.log > -------------------------------------------------------------- > ------------------------------------------- > /media/sf_DATA1/RETINOTOPY/IFEE2211 > Mon Mar 26 07:13:35 EDT 2012 > anadir = /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/rtopy.self.lh > DoGLMFit = 1 > DoContrasts = 1 > UpdateNeeded = 1 > ------------------------------------------ > ------- matlab output -------------------- > > < M A T L A B (R) > > Copyright 1984-2012 The MathWorks, Inc. > R2012a (7.14.0.739) 32-bit (glnx86) > February 9, 2012 > > > To get started, type one of these: helpwin, helpdesk, or demo. > For product information, visit www.mathworks.com. > > >> >> >> >> >> >> >> > /home/virtualuser/freesurfer/fsfast/toolbox/fast_selxavg3.m > >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> > > #@# IFEE2211 ############################### > /media/sf_DATA1/RETINOTOPY/IFEE2211 > ------------------------- > $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 > FreeSurfer Virtual Machine > sudo password: freesurfer > > FreeSurfer Virtual Machine > sudo password: freesurfer > > nruns = 4 > autostimdur = > > > outanadir = /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/rtopy.self.lh > > > FreeSurfer Virtual Machine > sudo password: > > Found 111344/120028 (92.8) voxels in mask > Creating Design Matrix > ... creation time = 0.007 sec > DoMCFit = 1 > ntptot = 492, nX = 36, DOF = 456 > Saving X matrix to > /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/rtopy.self.lh/Xtmp.mat > XCond = 1.20413 (normalized) > Computing contrast matrices > > > FreeSurfer Virtual Machine > sudo password: > > OLS Beta Pass > run 1 t= 0.0 > : > > FreeSurfer Virtual Machine > sudo password: > > ERROR: TR mismatch between analysis and data > analysis TR = 2, data TR = 0 > > > ------------------------------------------------------------------------ > *From:* Kiley Seymour <kiley_seym...@yahoo.com.au> > *To:* "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > *Sent:* Sunday, 25 March 2012 1:05 PM > *Subject:* Re: mkbrainmask-sess > > Hi again, > > Could this error be due to the fact that I don't have a full version > of fsl installed and configured on my ubuntu virtual machine? i.e. > does fsfast require fsl to be installed? > > Thanks > > K > > ------------------------------------------------------------------------ > *From:* Kiley Seymour <kiley_seym...@yahoo.com.au> > *To:* "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > *Sent:* Friday, 23 March 2012 3:04 PM > *Subject:* mkbrainmask-sess > > Dear Freesurfers, > > I am currently trying to do some retinotopic mapping. I have been > successful in running the reconstruction commands and setting > everything up for the analysis, but I have run into problems when > using the selxavg3-sess command. i.e. selxavg3-sess -a rtopy.self.lh > -s IFEE2211 -no-preproc ( -no-preproc since I have co-registered and > motion corrected my files in SPM). > > I was unable to run this command as freesurfer could not > find /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/001/global.meanval.dat > > So I ran mktemplate - sess, which was successfully completed. And then > I ran mkbrainmask-sess (see below). > > Any help with this would be much appreciated. > > Thanks > > Kiley > > > FreeSurfer:~/data1/RETINOTOPY> mkbrainmask-sess -s IFEE2211 -d > ~/data1/RETINOTOPY > ------------------------------------------------ > /media/sf_DATA1/RETINOTOPY/IFEE2211 > Fri Mar 23 09:42:26 EDT 2012 > mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil > 1 -nerode 0 > FSLMATHS fslmaths.fsl > Scratch Dir is /tmp/mkbrainmask_7930 > /media/sf_DATA1/RETINOTOPY/IFEE2211/bold > mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii > mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii > $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ > reading from template.nii.gz... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.998558, -0.0534653, -0.00482299) > j_ras = (-0.0536701, 0.992375, 0.110955) > k_ras = (0.00114604, -0.111054, 0.993814) > writing to /tmp/mkbrainmask_7930/in.nii... > # ---------- Using FSL's BET to Extract Brain------------------ # > /media/sf_DATA1/RETINOTOPY/IFEE2211/bold > bet.fsl /tmp/mkbrainmask_7930/in.nii /tmp/mkbrainmask_7930/brain -m -f 0.1 > /home/virtualuser/freesurfer/bin/bet.fsl: 150: /bin/remove_ext: not found > /home/virtualuser/freesurfer/bin/bet.fsl: 151: /bin/remove_ext: not found > /home/virtualuser/freesurfer/bin/bet.fsl: 158: /bin/imtest: not found > [: 158: =: unexpected operator > /home/virtualuser/freesurfer/bin/bet.fsl: 380: /bin/bet2: not found > mri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min .01 --o > /tmp/mkbrainmask_7930/brain_mask.nii > niiRead(): error opening file /tmp/mkbrainmask_7930/brain_mask.nii > > $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ > cwd /media/sf_DATA1/RETINOTOPY/IFEE2211/bold > cmdline mri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min > .01 --o /tmp/mkbrainmask_7930/brain_mask.nii > sysname Linux > hostname FreeSurfer > machine i686 > user virtualuser > > input /tmp/mkbrainmask_7930/brain_mask.nii > frame 0 > nErode3d 0 > nErode2d 0 > output /tmp/mkbrainmask_7930/brain_mask.nii > Binarizing based on threshold > min 0.01 > max +infinity > binval 1 > binvalnot 0 > > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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.
