is the command line that recon-all runs exactly the same as what you run? On Thu, 22 Aug 2013, Demian Wassermann wrote:

Hi Bruce,

No, but I was hoping not to have to run the whole process again (for all the subjects I need to relabel)

Thanks for the quick response

D

Demian Wassermann, PhD demian@bwh.harvard.edu LMI / PNL / SPL Labs Harvard Medical School Brigham and Women's Hospital 1249 Boylston, Boston, MA, USA http://lmi.bwh.harvard.edu/~wassermann/

On Aug 22, 2013, at 3:39 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

...

Hi Demian

does this happen if you run it through recon-all?

Bruce On Thu, 22 Aug 2013, Demian Wassermann wrote:

...

Dear Support line of free surfer,

I have a problem when I try to apply a new atlas to the surfaces. Even with the standard free surfer atlases it segfaults

Environment:

FREESURFER_HOME: /projects/schiz/software/freesurfer-v4.5/freesurfer

Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0

RedHat release: Fedora release 18 (Spherical Cow)

Kernel info: Linux 3.9.2-200.fc18.x86_64 x86_64

Command: $FREESURFER_HOME/bin/mris_ca_label -t $FREESURFER_HOME/average/colortable_desikan_killiany.txt case01009 lh lh.sphere.reg $FREESURFER_HOME/average/lh.curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs lh.test.annot

Output: $Id: mris_ca_label.c,v 1.23 2007/03/23 20:00:07 fischl Exp $ $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $ reading atlas from /projects/schiz/software/freesurfer-v4.5/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs... reading color table from GCSA file.... average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized Segmentation fault (core dumped)

Am I doing something wrong? How can I diagnose and fix this?

Thanks D

-- Demian Wassermann, PhD demian@bwh.harvard.edu LMI / PNL / SPL Labs Harvard Medical School Brigham and Women's Hospital 1249 Boylston, Boston, MA, USA http://lmi.bwh.harvard.edu/~wassermann/

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I do. You can look in the recon-all.log (or recon-all.cmd I think) and see if they are identical. If they are, make sure you are using the same binary On Thu, 22 Aug 2013, Demian Wassermann wrote:

How would I check this?

I thought you meant when I run

recon-all -autorecon-all -subjid case01009 -i my_t1.nii.gz

D

Demian Wassermann, PhD demian@bwh.harvard.edu LMI / PNL / SPL Labs Harvard Medical School Brigham and Women's Hospital 1249 Boylston, Boston, MA, USA http://lmi.bwh.harvard.edu/~wassermann/

On Aug 22, 2013, at 3:42 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

...

is the command line that recon-all runs exactly the same as what you run? On Thu, 22 Aug 2013, Demian Wassermann wrote:

...

Hi Bruce,

No, but I was hoping not to have to run the whole process again (for all the subjects I need to relabel)

Thanks for the quick response

D

Demian Wassermann, PhD demian@bwh.harvard.edu LMI / PNL / SPL Labs Harvard Medical School Brigham and Women's Hospital 1249 Boylston, Boston, MA, USA http://lmi.bwh.harvard.edu/~wassermann/

On Aug 22, 2013, at 3:39 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

...

Hi Demian

does this happen if you run it through recon-all?

Bruce On Thu, 22 Aug 2013, Demian Wassermann wrote:

...

Dear Support line of free surfer,

I have a problem when I try to apply a new atlas to the surfaces. Even with the standard free surfer atlases it segfaults

Environment:

FREESURFER_HOME: /projects/schiz/software/freesurfer-v4.5/freesurfer

Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0

RedHat release: Fedora release 18 (Spherical Cow)

Kernel info: Linux 3.9.2-200.fc18.x86_64 x86_64

Command: $FREESURFER_HOME/bin/mris_ca_label -t $FREESURFER_HOME/average/colortable_desikan_killiany.txt case01009 lh lh.sphere.reg $FREESURFER_HOME/average/lh.curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs lh.test.annot

Output: $Id: mris_ca_label.c,v 1.23 2007/03/23 20:00:07 fischl Exp $ $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $ reading atlas from /projects/schiz/software/freesurfer-v4.5/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs... reading color table from GCSA file.... average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized Segmentation fault (core dumped)

Am I doing something wrong? How can I diagnose and fix this?

Thanks D

-- Demian Wassermann, PhD demian@bwh.harvard.edu LMI / PNL / SPL Labs Harvard Medical School Brigham and Women's Hospital 1249 Boylston, Boston, MA, USA http://lmi.bwh.harvard.edu/~wassermann/

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