Hello,
I recently ran into issues using mri_convert on a CentOS 7 platform while having the same command work fine on CentOS 6. The error that results is:
Segmentation fault (core dumped)
I've tried on multiple machines with both operating systems to confirm the issue. I was wondering if you might have any insights or suggestions on how to fix this.
Thank you!
Danielle
________________________________
This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.
Hi Danielle
can you post the full command line and screen output?
cheers Bruce On Tue, 30 Jan 2018, Cooke,Danielle ( BIDMC - Neurology ) wrote:
Hello,
I recently ran into issues using mri_convert on a CentOS 7 platform while having the same command work fine on CentOS 6. The error that results is:
Segmentation fault (core dumped)
I've tried on multiple machines with both operating systems to confirm the issue. I was wondering if you might have any insights or suggestions on how to fix this.
Thank you!
Danielle
This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.
Hi Bruce,
This is the command and output on a CentOS 7 machine: [dc155@pinto DANI]$ mri_convert 3062.nii.gz -rl MNI152_T1_2mm_brain.nii.gz 3062_MNI.nii.gz mri_convert 3062.nii.gz -rl MNI152_T1_2mm_brain.nii.gz 3062_MNI.nii.gz $Id: mri_convert.c,v 1.146.2.1 2007/11/30 23:18:44 greve Exp $ reading from 3062.nii.gz... Segmentation fault (core dumped)
This is the command and output on a CentOS 6 machine: [dc155@door DANI]$ mri_convert 3062.nii.gz -rl MNI152_T1_2mm_brain.nii.gz 3062_MNI.nii.gz mri_convert 3062.nii.gz -rl MNI152_T1_2mm_brain.nii.gz 3062_MNI.nii.gz $Id: mri_convert.c,v 1.146.2.1 2007/11/30 23:18:44 greve Exp $ reading from 3062.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) reading template info from volume MNI152_T1_2mm_brain.nii.gz... Reslicing using trilinear interpolation writing to 3062_MNI.nii.gz...
Thank you, Danielle
On 1/30/18, 5:44 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
Hi Danielle
can you post the full command line and screen output?
cheers Bruce On Tue, 30 Jan 2018, Cooke,Danielle ( BIDMC - Neurology ) wrote:
> > Hello, > > > > I recently ran into issues using mri_convert on a CentOS 7 platform while having the same command work fine on CentOS 6. The > error that results is: > > Segmentation fault (core dumped) > > > > I've tried on multiple machines with both operating systems to confirm the issue. I was wondering if you might have any > insights or suggestions on how to fix this. > > > > Thank you! > > Danielle > > > > > _______________________________________________________________________________________________________________________________ > > This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is > privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, > any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, > please permanently delete it and immediately notify the sender. Thank you. > >
Hi Danielle
if you send me the two input volumes (don't cc the list) I'll see if we can replicate and fix this problem.
cheers Bruce On Wed, 31 Jan 2018, Cooke,Danielle ( BIDMC - Neurology ) wrote:
Hi Bruce,
This is the command and output on a CentOS 7 machine: [dc155@pinto DANI]$ mri_convert 3062.nii.gz -rl MNI152_T1_2mm_brain.nii.gz 3062_MNI.nii.gz mri_convert 3062.nii.gz -rl MNI152_T1_2mm_brain.nii.gz 3062_MNI.nii.gz $Id: mri_convert.c,v 1.146.2.1 2007/11/30 23:18:44 greve Exp $ reading from 3062.nii.gz... Segmentation fault (core dumped)
This is the command and output on a CentOS 6 machine: [dc155@door DANI]$ mri_convert 3062.nii.gz -rl MNI152_T1_2mm_brain.nii.gz 3062_MNI.nii.gz mri_convert 3062.nii.gz -rl MNI152_T1_2mm_brain.nii.gz 3062_MNI.nii.gz $Id: mri_convert.c,v 1.146.2.1 2007/11/30 23:18:44 greve Exp $ reading from 3062.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) reading template info from volume MNI152_T1_2mm_brain.nii.gz... Reslicing using trilinear interpolation writing to 3062_MNI.nii.gz...
Thank you, Danielle
On 1/30/18, 5:44 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
Hi Danielle
can you post the full command line and screen output?
cheers Bruce On Tue, 30 Jan 2018, Cooke,Danielle ( BIDMC - Neurology ) wrote:
Hello,
I recently ran into issues using mri_convert on a CentOS 7 platform while having the same command work fine on CentOS 6. The error that results is:
Segmentation fault (core dumped)
I've tried on multiple machines with both operating systems to confirm the issue. I was wondering if you might have any insights or suggestions on how to fix this.
Thank you!
Danielle
This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Cooke,Danielle ( BIDMC - Neurology )