Hi Michelle, did you change the structural after you ran the retinotopy analysis? It looks like the number of vertices changed. If so, then you'll need to re-run the fMRI analysis. doug
Michelle Umali wrote: > Dear Freesurfers, > I am working on a retinotopy analysis and I got this error: > ERROR: dimension mismatch between mask and surf when trying to look at > map angle in tksurfer-sess > Do I need to add --reshape flag? If so, where? > > Any help would be most appreciated. > Thanks. > Michelle > > Here are the analysis commands I used the error output for viewing the > map is below it : > mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 -retinotopy 48 > -paradigm rtopy.par -nskip 4 -fwhm 0 -fsd bold -force > > > mkanalysis-sess -a rtopy.self.rh -surface self rh -TR 2 -retinotopy 48 > -paradigm rtopy.par -nskip 4 -fwhm 0 -fsd bold -force > > > > preproc-sess -surface self lhrh -fwhm 5 -per-run -s sj07 -fsd bold -force > > > > selxavg3-sess -a rtopy.self.lh -s sj07 -force > > selxavg3-sess -a rtopy.self.rh -s sj07 -force > > fieldsign-sess -a rtopy.self.lh -occip -s sj07 > fieldsign-sess -a rtopy.self.rh -occip -s sj07 > > This is the output when I tried to view in tksurfer-sess > > BOTANICA:/usr/local/freesurfer/subjects/retinotopy> tksurfer-sess -a > rtopy.self.lh -s sj07 -map angle > Surface self lh > Map Surface self lh > $Id: tksurfer-sess,v 1.16.2.1 2011/04/05 22:25:15 greve Exp $ > Linux BOTANICA 2.6.32-33-generic #70-Ubuntu SMP Thu Jul 7 21:13:52 UTC > 2011 x86_64 GNU/Linux > Tue Sep 27 06:37:33 EDT 2011 > /usr/local/freesurfer/bin/tksurfer > > list eccen polar > con/map eccen > /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/eccen/angle.nii.gz > con/map polar > /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/polar/angle.nii.gz > maplist > /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/eccen/angle.nii.gz > /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/polar/angle.nii.gz > mri_concat > /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/eccen/angle.nii.gz > /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/polar/angle.nii.gz > --o > /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/tksconcat.nii > ninputs = 2 > Checking inputs > nframestot = 2 > Allocing output > Done allocing > nframes = 2 > Writing to > /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/tksconcat.nii > cd /usr/local/freesurfer/subjects/retinotopy > setenv SUBJECTS_DIR /usr/local/freesurfer/subjects > tksurfer ld07 lh inflated -overlay > /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/tksconcat.nii > -label-outline -colscalebarflag 1 -annot aparc -fthresh 2 -fmid > 3.00000000000000000000 -fslope .50000000000000000000 -mask > /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/fieldsign/fsig.nii.gz > -mask-thresh 2 -fthresh .01 > > Contrasts > 0 eccen > 1 polar > > > setting colscalebarflag to 1 > setting fthresh to 2.0000 > setting fmid to 3.0000 > setting fslope to 0.5000 > mrismaskfile > /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/fieldsign/fsig.nii.gz... > setting mrismaskthresh to 2.0000 > setting fthresh to 0.0100 > subject is ld07 > hemi is lh > surface is inflated > surfer: current subjects dir: /usr/local/freesurfer/subjects > surfer: not in "scripts" dir ==> using cwd for session root > surfer: session root data dir ($session) set to: > surfer: /usr/local/freesurfer/subjects/retinotopy > checking for nofix files in 'inflated' > Reading image info (/usr/local/freesurfer/subjects/ld07) > Reading /usr/local/freesurfer/subjects/ld07/mri/orig.mgz > surfer: Reading header info from > /usr/local/freesurfer/subjects/ld07/mri/orig.mgz > surfer: vertices=156145, faces=312286 > tkmedit: Trying to open > /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/tksconcat.dat > surfer: Interpreting overlay volume > /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/tksconcat.nii > as registered functional volume. > surfer: curvature read: min=-3.127128 max=2.364444 > reading colortable from annotation file... > colortable with 36 entries read (originally > /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) > Found embedded color table in annotation. > 8162 vertices did not have an annotation! > surfer: single buffered window > surfer: tkoInitWindow(ld07) > Reading mris mask > /usr/local/freesurfer/subjects/retinotopy/sj07/bold/rtopy.self.lh/fieldsign/fsig.nii.gz > ERROR: dimension mismatch between mask and surf > _______________________________________________ > 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.
