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 > 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. > > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.