On Wed, 14 Oct 2015,
Syeda Maryam wrote:

> So for some reason my mail with the attachments won't get delivered...the
> message size exceeds the limits. I was wondering if the segmentation fault
> error I'm getting might be do to some problem in the freesurfer version I'm
> running?
>
> Thanks,
> Syeda
>
>
>
> On Wednesday, October 14, 2015 12:09 PM, Syeda Maryam <swajiham@yahoo.com>
> wrote:
>
>
> I'm not sure if my last message got delivered or not so I'll resend it.
>     
>     Thanks very much for looking into this so quickly. Sure thing! I've
> attached the images here. The aseg file opens up with freeview, and the
> mri_label2vol command works fine     on my local machine but when I try to
> implement it on our server using nipype, it gives me the error I mentioned.
>
>     Best,
>     Syeda
>
>
>
> On Wednesday, October 14, 2015 11:56 AM, Syeda Maryam <swajiham@yahoo.com>
> wrote:
>
>
> Thanks very much for looking into this so quickly. Sure thing! I've attached
> the images here. The aseg file opens up with freeview, and the mri_label2vol
> command works fine on my local machine but when I try to implement it on our
> server using nipype, it gives me the error I mentioned.
>
> Best,
> Syeda
>
>
>
> On Wednesday, October 14, 2015 11:50 AM, Bruce Fischl
> <fischl@nmr.mgh.harvard.edu> wrote:
>
>
> Hi Syeda
>
> that commnand doesn't segfault when I try it on another subject here. If
> you email me the aseg.mgz and the rawavg.mgz I'll take a look
>
> cheers
> Bruce
>
> On Wed, 14 Oct 2015, Syeda
> Maryam wrote:
>
> > Hello Freesurfer experts,
> >
> > I'm getting a segmentation fault when I use the mri_label2vol command to
> push aseg labels from freesurfer space to my
> > subject's original T1 space (using the example given on the freesurfer
> website). I'm not sure why this is
> > happening...I've tried changing the parameters countless times but nothing
> has worked. I also checked my "aseg.mgz" to
> > make sure it's not corrupted but that isn't the issue either. Any help
> would be highly appreciated!! Thanks in advance
> >
> > mri_label2vol --regheader /scratch/o/olegm/olegm/2015/test_waj/aseg.mgz
> --seg /tmp/tmpUj4qzA/aseg2raw/aseg.mgz --temp
> > /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz --o
> /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
> > Number of labels: 0
> > Annot File:      (null)
> > Template Volume: /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz
> > Outut Volume: /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
> > Registration File: (null)
> > Fill Threshold: 0
> > Label Vox Vol:  1
> > ProjType:       (null)
> > ProjTypeId:     0
> > ProjStart:      0
> > ProjStop:       0
> > ProjDelta:      0.1
> > Subject:  (null)
> > Hemi:     (null)
> > UseNewASeg2Vol:  1
> > DoLabelStatVol  0
> > LabelCodeOffset  0
> > setenv SUBJECTS_DIR /scratch/o/olegm/olegm/subjects
> > $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $
> > Template RAS-to-Vox: --------
> > -0.985   0.000   0.000   128.000;
> > -0.000  -0.000  -0.985   128.000;
> > -0.000   0.833  -0.000   98.000;
> >  0.000   0.000   0.000   1.000;
> > Template Voxel Volume: 1.23773
> > nHits Thresh: 0
> > Computing registration based on header
> > RegMat: --------
> >  1.000   0.000   0.000  -0.000;
> >  0.000   1.000   0.000   0.000;
> >  0.000   0.000   1.000   0.000;
> >  0.000   0.000   0.000   1.000;
> > Label RAS-to-Vox: --------
> > -0.985   0.000   0.000   128.000;
> >  0.000   0.000  -0.985   128.000;
> >  0.000   0.833   0.000   98.000;
> >  0.000   0.000   0.000   1.000;
> > ASeg2Vol: Building LUT
> > Segmentation fault
>
> >
> >
> >
>
>
> 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.
>
>
>
>
>
>
>
>

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.