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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
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.
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 greve@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
The gcareg step depends on the talairach registration, so if that is changed, it thinks that the gcareg needs to change. If the gcareg needs to change, then the canorm needs to change, and so on. This does not mean that anything really needs to be updated. This is strictly looking at the time stamps and assuming that things have changed and need to be updated. If your results look ok, then there's no need to re-run.
Unfortunately, this does not tell us whether the surfaces themselves are up to date. You can do this with: recon-all -vno-check -s subject This looks at the number of vertices in each of the surfaces to make sure they are consistent.
doug
Michelle Umali wrote:
Hey Doug and Freesurfers, At the bottom is the output showing what steps didn't run.
- 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.
- 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 mailto: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 mailto: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
mailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://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
Hi Doug and Freesurfers, I ran the -vno-check and the number of vertices matches for left and right hemispheres (see below):
Since all there are an equal number of vertices, how is the mismatch error occurring in fieldsign-sess and how do I get it to run?
Thanks for all your help. Michelle
vno_match_check ld07 lh Checking ld07/surf/lh.orig... Checking ld07/surf/lh.white... Checking ld07/surf/lh.pial... Checking ld07/surf/lh.inflated... Checking ld07/surf/lh.smoothwm... Checking ld07/surf/lh.sphere... Checking ld07/surf/lh.curv... Checking ld07/surf/lh.sulc... Checking ld07/surf/lh.area... Checking ld07/surf/lh.thickness... Checking ld07/label/lh.aparc.annot... Checking ld07/label/lh.aparc.a2009s.annot... Pass: all surfaces and surface data for subject ld07 have the same number of vertices.
The same is true for the right hemisphere.
On Wed, Sep 28, 2011 at 5:21 PM, Douglas N Greve <g reve@nmr.mgh.harvard.edu
wrote:
The gcareg step depends on the talairach registration, so if that is changed, it thinks that the gcareg needs to change. If the gcareg needs to change, then the canorm needs to change, and so on. This does not mean that anything really needs to be updated. This is strictly looking at the time stamps and assuming that things have changed and need to be updated. If your results look ok, then there's no need to re-run.
Unfortunately, this does not tell us whether the surfaces themselves are up to date. You can do this with: recon-all -vno-check -s subject This looks at the number of vertices in each of the surfaces to make sure they are consistent.
doug
Michelle Umali wrote:
Hey Doug and Freesurfers, At the bottom is the output showing what steps didn't run.
- 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.
- 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 <mailto:greve@nmr.mgh.harvard.**edugreve@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 <mailto:greve@nmr.mgh.harvard.**edugreve@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 <mailto:Freesurfer@nmr.mgh.**
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>>>-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<
http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html<
http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<
http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html<
http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://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/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Michelle Umali