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 <swaji...@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 <swaji...@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
<fis...@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
>
>
>
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