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
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
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 greve@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
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