On Wed, 14 Oct 2015, Syeda Maryam wrote:

> Hi Bruce,
> I just sent you the files on filedrop! I thought it might have something to do with the freesurfer version since the
> mri_label2vol comman works fine on my local machine and the segmentation fault I was talking about only happens when I
> try to run it on the server our research group is using. But when I checked the freesurfer versions, turns out the same
> version is installed on both machines: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
>
> Needless to say, I'm well and truly stumped right now.
> Really appreciate your help in this matter!
>
> Best,
> Syeda
>
>
>
>
>
> On Wednesday, October 14, 2015 12:20 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
>
>
> it's possible, or something to do with your images. You can use either
> our filedrop or ftp site to send them to me if you want
> 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
> >
> > >
> > >
> > >
> >
> >
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> >
> >
> >
> >
> >
>
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