Hey Doug and Freesurfers, At the bottom is the output showing what steps didn't run.
1) Do you think I did the whole recon-all pipeline wrong? Here's what i did after I originally ran recon-all -all -label_v1:
I made edits with talairach registration edits with tkregister2 and ran recon-all -all -label_v1. After that,with tkmedit I made edits to brainmask.mgz and wm-mgz, then recon-all -autorecon2-wm and autorecon 3, -label_v1.
2) Was adding the -label_v1 flag what caused the below steps to not happen and cause the mismatch? Does adding the -label_v1 flag cause recon-all to not run on the rest of the brain? If so, do I just run recon-all -autorecon2 and -autorecon3 without the -label_v1 flag?
Thanks. Michelle
FreeSurfer:/media/sf_windows/ subjects> recon-all -s ld07 -make all -dontrun INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 Subject 'ld07': make -n all recon-all -s /media/sf_windows/subjects/ld07 -gcareg recon-all -s /media/sf_windows/subjects/ld07 -canorm recon-all -s /media/sf_windows/subjects/ld07 -careg -careginv recon-all -s /media/sf_windows/subjects/ld07 -rmneck recon-all -s /media/sf_windows/subjects/ld07 -skull-lta recon-all -s /media/sf_windows/subjects/ld07 -calabel recon-all -s /media/sf_windows/subjects/ld07 -normalization2 recon-all -s /media/sf_windows/subjects/ld07 -maskbfs recon-all -s /media/sf_windows/subjects/ld07 -segmentation recon-all -s /media/sf_windows/subjects/ld07 -fill recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -tessellate recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -tessellate recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -smooth1 recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -smooth1 recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -inflate1 recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -inflate1 recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -qsphere recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -qsphere recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -fix recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -fix recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -white recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -white recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -white recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -white recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -white recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -white recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -smooth2 recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -smooth2 recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -inflate2 recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -inflate2 recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -inflate2 recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -inflate2 recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -sphere recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -sphere recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -surfreg recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -surfreg recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -jacobian_white recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -jacobian_white recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -avgcurv recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -avgcurv recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -cortparc recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -cortparc recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -pial recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -pial recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -pial recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -pial recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -parcstats recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -parcstats recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -cortparc2 recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -cortparc2 recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -parcstats2 recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -parcstats2 recon-all -s /media/sf_windows/subjects/ld07 -hemi lh -cortribbon recon-all -s /media/sf_windows/subjects/ld07 -hemi rh -cortribbon recon-all -s /media/sf_windows/subjects/ld07 -segstats recon-all -s /media/sf_windows/subjects/ld07 -aparc2aseg recon-all -s /media/sf_windows/subjects/ld07 -wmparc - Hide quoted text -
On Wed, Sep 28, 2011 at 11:21 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Hi Michelle, this almost surely means that the surfaces are out-of-synch. You can try recon-all -s subject -make all -dontrun on one of your subjects.
If everything is in synch, then it should print make: Nothing to be done for `all'.
If not, it should print out the steps that it would have run (if not for
the
-dontrun option).
doug
Michelle Umali wrote:
Hi Doug, I get the same MRISripZeros() and MRIScopyMRI Surf/src mismatch error when I use -sphere and not -occip in fieldsign-sess.
What else should I try?
Thank you. Michelle
On Tue, Sep 27, 2011 at 8:51 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Is the occip patch out of synch with the subject? Does it run if you use -sphere instead of -occip? doug
Michelle Umali wrote:
Dear Freesurfers, This is related to my retinotopy analysis tksurfer-sess dimension mismatch error message.
So another subject had these errors come up during fieldsign-sess selxavg3-sess -a rtopy.self.lh -s sjXX -force (which ran without error)
then I ran fieldsign fieldsign-sess -a rtopy.self.lh -occip -s sjXX
and got: ERROR: MRISripZeros(): dimension mismatch ERROR: MRIScopyMRI: Surf/Src dimension mismatch. ERROR: MRIScopyMRI: Surf/Src dimension mismatch. ERROR: MRIScopyMRI: Surf/Src dimension mismatch. ERROR: MRIScopyMRI: Surf/Src dimension mismatch.
What may have caused this?
Thanks. Michelle _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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