Dear FS experts,
I've installed freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 and I'm trying to run bbregister to register a AV45-PET image to its corresponding FS processed T1 image. For that, I'm trying to run:
bbregister --s SUBJ_ID --mov SUBJ_PET --reg register.dat --init-fsl --t1
And I keep getting segfaults:
Log file is register.dat.log dom jul 24 16:44:19 CEST 2016
$Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $ Linux fredlab 3.16.0-30-generic #40~14.04.1-Ubuntu SMP Thu Jan 15 17:43:14 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz ./tmp.bbregister.5353/template.nii mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz ./tmp.bbregister.5353/template.nii Segmentation fault (core dumped)
I have tried the same installation and command in two different computers and obtained the same segfault. I have also tried the same pipeline using instead the FS version freesurfer-Linux-centos4-stable-pub-v5.1.0.tar.gz and get the same result. I didn't have this issue using freesurfer 5.3, but I need to use 5.1 for an ongoing project.
I'm in an Ubuntu 14.04 LTS with 3.6GB of Memory, Processor Intel Core 2 Duo 3.0GHz, Graphics Intel Q45/Q43 OS type 64 bits.
Any help would be much appreciated,
Thanks a lot in advance,
Fred Sampedro
It looks like one of two things:
1. The files SUBJ_ID.nii.gz is corrupted. See if another tool (FSL, SPM, AFNI) can read the file
2. You have run out of disk space
On 7/24/16 10:52 AM, Fred Sampedro wrote:
Dear FS experts,
I've installed freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 and I'm trying to run bbregister to register a AV45-PET image to its corresponding FS processed T1 image. For that, I'm trying to run:
bbregister --s SUBJ_ID --mov SUBJ_PET --reg register.dat --init-fsl --t1
And I keep getting segfaults:
Log file is register.dat.log dom jul 24 16:44:19 CEST 2016
$Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $ Linux fredlab 3.16.0-30-generic #40~14.04.1-Ubuntu SMP Thu Jan 15 17:43:14 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz ./tmp.bbregister.5353/template.nii mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz ./tmp.bbregister.5353/template.nii Segmentation fault (core dumped)
I have tried the same installation and command in two different computers and obtained the same segfault. I have also tried the same pipeline using instead the FS version freesurfer-Linux-centos4-stable-pub-v5.1.0.tar.gz and get the same result. I didn't have this issue using freesurfer 5.3, but I need to use 5.1 for an ongoing project.
I'm in an Ubuntu 14.04 LTS with 3.6GB of Memory, Processor Intel Core 2 Duo 3.0GHz, Graphics Intel Q45/Q43 OS type 64 bits.
Any help would be much appreciated,
Thanks a lot in advance,
Fred Sampedro
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Douglas,
Thank you very much for answering. Unfortunately, I can read all the files without any problem in FSL/SPM, and I still have more than 40GB of free space. In fact, running the exact same instruction in freesurfer 5.3 works fine.
:(
On Mon, Jul 25, 2016 at 5:21 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
It looks like one of two things:
- The files SUBJ_ID.nii.gz is corrupted. See if another tool (FSL, SPM,
AFNI) can read the file
- You have run out of disk space
On 7/24/16 10:52 AM, Fred Sampedro wrote:
Dear FS experts,
I've installed freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 and I'm trying to run bbregister to register a AV45-PET image to its corresponding FS processed T1 image. For that, I'm trying to run:
bbregister --s SUBJ_ID --mov SUBJ_PET --reg register.dat --init-fsl --t1
And I keep getting segfaults:
Log file is register.dat.log dom jul 24 16:44:19 CEST 2016
$Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $ Linux fredlab 3.16.0-30-generic #40~14.04.1-Ubuntu SMP Thu Jan 15 17:43:14 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz ./tmp.bbregister.5353/template.nii mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz ./tmp.bbregister.5353/template.nii Segmentation fault (core dumped)
I have tried the same installation and command in two different computers and obtained the same segfault. I have also tried the same pipeline using instead the FS version freesurfer-Linux-centos4-stable-pub-v5.1.0.tar.gz and get the same result. I didn't have this issue using freesurfer 5.3, but I need to use 5.1 for an ongoing project.
I'm in an Ubuntu 14.04 LTS with 3.6GB of Memory, Processor Intel Core 2 Duo 3.0GHz, Graphics Intel Q45/Q43 OS type 64 bits.
Any help would be much appreciated,
Thanks a lot in advance,
Fred Sampedro
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Sorry, I have no idea and I'm not going to try to dig in to 5.1 to see. You can just copy mri_convert from 5.3 into 5.1 (make a backup first)
On 7/25/16 12:31 PM, Fred Sampedro wrote:
Hi Douglas,
Thank you very much for answering. Unfortunately, I can read all the files without any problem in FSL/SPM, and I still have more than 40GB of free space. In fact, running the exact same instruction in freesurfer 5.3 works fine.
:(
On Mon, Jul 25, 2016 at 5:21 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
It looks like one of two things: 1. The files SUBJ_ID.nii.gz is corrupted. See if another tool (FSL, SPM, AFNI) can read the file 2. You have run out of disk space On 7/24/16 10:52 AM, Fred Sampedro wrote:Dear FS experts, I've installed freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 and I'm trying to run bbregister to register a AV45-PET image to its corresponding FS processed T1 image. For that, I'm trying to run: bbregister --s SUBJ_ID --mov SUBJ_PET --reg register.dat --init-fsl --t1 And I keep getting segfaults: Log file is register.dat.log dom jul 24 16:44:19 CEST 2016 $Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $ Linux fredlab 3.16.0-30-generic #40~14.04.1-Ubuntu SMP Thu Jan 15 17:43:14 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz ./tmp.bbregister.5353/template.nii mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz ./tmp.bbregister.5353/template.nii Segmentation fault (core dumped) I have tried the same installation and command in two different computers and obtained the same segfault. I have also tried the same pipeline using instead the FS version freesurfer-Linux-centos4-stable-pub-v5.1.0.tar.gz and get the same result. I didn't have this issue using freesurfer 5.3, but I need to use 5.1 for an ongoing project. I'm in an Ubuntu 14.04 LTS with 3.6GB of Memory, Processor Intel Core 2 Duo 3.0GHz, Graphics Intel Q45/Q43 OS type 64 bits. Any help would be much appreciated, Thanks a lot in advance, Fred Sampedro _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
Hi Douglas,
Thanks a lot for your help, I understand. I tried replacing the mri_convert in 5.1 from the 5.3 and the bbregister command went a little bit further. Unfortunately, it segfaulted again when computing the relative costs.
I'm attaching the output of the same command in 5.3 and in 5.1. Until the "Loading mov" in line 210, the output is actually the same. Could it be related to errors regarding the reading of the PET image?
If anyone could help me figuring out which instruction is failing so I could try to replace it with the 5.3 version I would be very grateful.
Thanks a lot in advance,
Fred
On Tue, Jul 26, 2016 at 1:30 AM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Sorry, I have no idea and I'm not going to try to dig in to 5.1 to see. You can just copy mri_convert from 5.3 into 5.1 (make a backup first)
On 7/25/16 12:31 PM, Fred Sampedro wrote:
Hi Douglas,
Thank you very much for answering. Unfortunately, I can read all the files without any problem in FSL/SPM, and I still have more than 40GB of free space. In fact, running the exact same instruction in freesurfer 5.3 works fine.
:(
On Mon, Jul 25, 2016 at 5:21 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
It looks like one of two things:
- The files SUBJ_ID.nii.gz is corrupted. See if another tool (FSL, SPM,
AFNI) can read the file
- You have run out of disk space
On 7/24/16 10:52 AM, Fred Sampedro wrote:
Dear FS experts,
I've installed freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 and I'm trying to run bbregister to register a AV45-PET image to its corresponding FS processed T1 image. For that, I'm trying to run:
bbregister --s SUBJ_ID --mov SUBJ_PET --reg register.dat --init-fsl --t1
And I keep getting segfaults:
Log file is register.dat.log dom jul 24 16:44:19 CEST 2016
$Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $ Linux fredlab 3.16.0-30-generic #40~14.04.1-Ubuntu SMP Thu Jan 15 17:43:14 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz ./tmp.bbregister.5353/template.nii mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz ./tmp.bbregister.5353/template.nii Segmentation fault (core dumped)
I have tried the same installation and command in two different computers and obtained the same segfault. I have also tried the same pipeline using instead the FS version freesurfer-Linux-centos4-stable-pub-v5.1.0.tar.gz and get the same result. I didn't have this issue using freesurfer 5.3, but I need to use 5.1 for an ongoing project.
I'm in an Ubuntu 14.04 LTS with 3.6GB of Memory, Processor Intel Core 2 Duo 3.0GHz, Graphics Intel Q45/Q43 OS type 64 bits.
Any help would be much appreciated,
Thanks a lot in advance,
Fred Sampedro
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
I have no idea. You can try copying the 5.3 version of mri_segreg to 5.1
On 07/28/2016 04:10 AM, Fred Sampedro wrote:
Hi Douglas,
Thanks a lot for your help, I understand. I tried replacing the mri_convert in 5.1 from the 5.3 and the bbregister command went a little bit further. Unfortunately, it segfaulted again when computing the relative costs.
I'm attaching the output of the same command in 5.3 and in 5.1. Until the "Loading mov" in line 210, the output is actually the same. Could it be related to errors regarding the reading of the PET image?
If anyone could help me figuring out which instruction is failing so I could try to replace it with the 5.3 version I would be very grateful.
Thanks a lot in advance,
Fred
On Tue, Jul 26, 2016 at 1:30 AM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Sorry, I have no idea and I'm not going to try to dig in to 5.1 to see. You can just copy mri_convert from 5.3 into 5.1 (make a backup first) On 7/25/16 12:31 PM, Fred Sampedro wrote:Hi Douglas, Thank you very much for answering. Unfortunately, I can read all the files without any problem in FSL/SPM, and I still have more than 40GB of free space. In fact, running the exact same instruction in freesurfer 5.3 works fine. :( On Mon, Jul 25, 2016 at 5:21 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: It looks like one of two things: 1. The files SUBJ_ID.nii.gz is corrupted. See if another tool (FSL, SPM, AFNI) can read the file 2. You have run out of disk space On 7/24/16 10:52 AM, Fred Sampedro wrote:Dear FS experts, I've installed freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 and I'm trying to run bbregister to register a AV45-PET image to its corresponding FS processed T1 image. For that, I'm trying to run: bbregister --s SUBJ_ID --mov SUBJ_PET --reg register.dat --init-fsl --t1 And I keep getting segfaults: Log file is register.dat.log dom jul 24 16:44:19 CEST 2016 $Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $ Linux fredlab 3.16.0-30-generic #40~14.04.1-Ubuntu SMP Thu Jan 15 17:43:14 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz ./tmp.bbregister.5353/template.nii mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz ./tmp.bbregister.5353/template.nii Segmentation fault (core dumped) I have tried the same installation and command in two different computers and obtained the same segfault. I have also tried the same pipeline using instead the FS version freesurfer-Linux-centos4-stable-pub-v5.1.0.tar.gz and get the same result. I didn't have this issue using freesurfer 5.3, but I need to use 5.1 for an ongoing project. I'm in an Ubuntu 14.04 LTS with 3.6GB of Memory, Processor Intel Core 2 Duo 3.0GHz, Graphics Intel Q45/Q43 OS type 64 bits. Any help would be much appreciated, Thanks a lot in advance, Fred Sampedro _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Douglas N Greve
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Fred Sampedro