Hi Doug, I didn't change the structural after the analysis. Before the retinotopy analysis, I ran recon-all -all, made some brainmask and white matter edits, them ran autorecon2-wm and autorecon3. Finally, I made occipital patches, then flattened them with mris_flatten.
When I ran this all before using Freesurfer 5.0 I did not encounter this problem. The only difference is that this time I made brainmask and white matter edits during the recon-all process to get better results. Every other step is the same. I am grateful for any suggestions. Thanks. Michelle . On Tuesday, September 27, 2011, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > 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/fie _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer < 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 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > 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. > >
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