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
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.
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
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.
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
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.
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 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
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.
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 fischl@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 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
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.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Syeda Maryam