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