So the strangest thing happened. Just on a hunch, I logged out of the server
then logged back in, and now it's running! It's a mystery to me. Thanks again,
I'll check the RAM specs and get back to you. For now though it seems to be
working. Hope it stays that way!
Best,Syeda
On Wednesday, October 14, 2015 12:48 PM, Bruce Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
Hi Syeda
it doesn't die when I run it locally. How much RAM do you have on the
machine that it crashes on? If you want a new version we can send you one.
cheers
Bruce
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
> <fis...@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 <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
> >
> > >
> > >
> > >
> >
> >
> > The information in this e-mail is intended only for the person to whom it is
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> > dispose of the e-mail.
> >
> >
> >
> >
> >
> >
> >
> >
>
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