Hello freesurfer experts,
I am trying to use an occipital lobe template adapted to my data as several surface and volume files, and there seems to be a problem with the surface files. Whenever I try to open a surface overlay (in .mgz format) in freeview this error comes up;
freadFloat: fread failed freadFloat: fread failed ... [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range ...
When I try to convert this file to nifti format a seemingly similar error comes up;
(...) mri_convert rh.template_areas.mgz AU_areas_template_rh.nii.gz mri_convert.bin rh.template_areas.mgz AU_areas_template_rh.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from rh.template_areas.mgz... TR=0.00, 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) writing to AU_areas_template_rh.nii.gz... NIFTI FORMAT ERROR: nslices 117239 in volume exceeds 32768
I have tried to debug but failed so far. Has anyone come across a similar problem and do you have an opinion onto what might be causing this? The same adapted template's volume files work just fine.
--I am using Ubuntu 16.04& freesurfer v.6
Thank you so much! Idil
Hi Idil,
we only store surface overlays in .mgz not surfaces themselves. Try loading a surface (like lh.inflated) then load whatever you were looking at as an overlay on the surface cheers Bruce On Mon, 24 Jul 2017, Yagmur Ozdemir 19 wrote:
Hello freesurfer experts,
I am trying to use an occipital lobe template adapted to my data as several surface and volume files, and there seems to be a problem with the surface files. Whenever I try to open a surface overlay (in .mgz format) in freeview this error comes up;
freadFloat: fread failed freadFloat: fread failed ... [0]PETSC ERROR:
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range ...
When I try to convert this file to nifti format a seemingly similar error comes up;
(...) mri_convert rh.template_areas.mgz AU_areas_template_rh.nii.gz mri_convert.bin rh.template_areas.mgz AU_areas_template_rh.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from rh.template_areas.mgz... TR=0.00, 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) writing to AU_areas_template_rh.nii.gz... NIFTI FORMAT ERROR: nslices 117239 in volume exceeds 32768
I have tried to debug but failed so far. Has anyone come across a similar problem and do you have an opinion onto what might be causing this? The same adapted template's volume files work just fine.
--I am using Ubuntu 16.04& freesurfer v.6
Thank you so much! Idil
Bruce,
Thank you so much for the help! I guess then the way to export these overlays to other softwares is writing them on the subject's inflated surface file.
Best, Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, July 24, 2017 10:36 PM To: Freesurfer support list Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
Hi Idil,
we only store surface overlays in .mgz not surfaces themselves. Try loading a surface (like lh.inflated) then load whatever you were looking at as an overlay on the surface cheers Bruce On Mon, 24 Jul 2017, Yagmur Ozdemir 19 wrote:
Hello freesurfer experts,
I am trying to use an occipital lobe template adapted to my data as several surface and volume files, and there seems to be a problem with the surface files. Whenever I try to open a surface overlay (in .mgz format) in freeview this error comes up;
freadFloat: fread failed freadFloat: fread failed ... [0]PETSC ERROR:
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range ...
When I try to convert this file to nifti format a seemingly similar error comes up;
(...) mri_convert rh.template_areas.mgz AU_areas_template_rh.nii.gz mri_convert.bin rh.template_areas.mgz AU_areas_template_rh.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from rh.template_areas.mgz... TR=0.00, 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) writing to AU_areas_template_rh.nii.gz... NIFTI FORMAT ERROR: nslices 117239 in volume exceeds 32768
I have tried to debug but failed so far. Has anyone come across a similar problem and do you have an opinion onto what might be causing this? The same adapted template's volume files work just fine.
--I am using Ubuntu 16.04& freesurfer v.6
Thank you so much! Idil
_______________________________________________ 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 Idil
I'm not sure what you mean. If you give us a better idea of your overall goal we can give you more helpful answers I expect Bruce On Tue, 25 Jul 2017, Yagmur Ozdemir 19 wrote:
Bruce,
Thank you so much for the help! I guess then the way to export these overlays to other softwares is writing them on the subject's inflated surface file.
Best, Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, July 24, 2017 10:36 PM To: Freesurfer support list Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
Hi Idil,
we only store surface overlays in .mgz not surfaces themselves. Try loading a surface (like lh.inflated) then load whatever you were looking at as an overlay on the surface cheers Bruce On Mon, 24 Jul 2017, Yagmur Ozdemir 19 wrote:
Hello freesurfer experts,
I am trying to use an occipital lobe template adapted to my data as several surface and volume files, and there seems to be a problem with the surface files. Whenever I try to open a surface overlay (in .mgz format) in freeview this error comes up;
freadFloat: fread failed freadFloat: fread failed ... [0]PETSC ERROR:
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range ...
When I try to convert this file to nifti format a seemingly similar error comes up;
(...) mri_convert rh.template_areas.mgz AU_areas_template_rh.nii.gz mri_convert.bin rh.template_areas.mgz AU_areas_template_rh.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from rh.template_areas.mgz... TR=0.00, 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) writing to AU_areas_template_rh.nii.gz... NIFTI FORMAT ERROR: nslices 117239 in volume exceeds 32768
I have tried to debug but failed so far. Has anyone come across a similar problem and do you have an opinion onto what might be causing this? The same adapted template's volume files work just fine.
--I am using Ubuntu 16.04& freesurfer v.6
Thank you so much! Idil
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
I am trying to export the overlays in .mgz format to Brainvoyager which recognizes nifti or its native .vmr format. However the mri_convert command gives error when I try to convert the templates. I thought if I could save the overlays directly onto the inflated surface files I could convert then visualize them in Brainvoyager, but couldn't figure that out so far. Thank you for the help!
Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Tuesday, July 25, 2017 7:47 PM To: Freesurfer support list Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
Hi Idil
I'm not sure what you mean. If you give us a better idea of your overall goal we can give you more helpful answers I expect Bruce On Tue, 25 Jul 2017, Yagmur Ozdemir 19 wrote:
Bruce,
Thank you so much for the help! I guess then the way to export these overlays to other softwares is writing them on the subject's inflated surface file.
Best, Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, July 24, 2017 10:36 PM To: Freesurfer support list Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
Hi Idil,
we only store surface overlays in .mgz not surfaces themselves. Try loading a surface (like lh.inflated) then load whatever you were looking at as an overlay on the surface cheers Bruce On Mon, 24 Jul 2017, Yagmur Ozdemir 19 wrote:
Hello freesurfer experts,
I am trying to use an occipital lobe template adapted to my data as several surface and volume files, and there seems to be a problem with the surface files. Whenever I try to open a surface overlay (in .mgz format) in freeview this error comes up;
freadFloat: fread failed freadFloat: fread failed ... [0]PETSC ERROR:
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range ...
When I try to convert this file to nifti format a seemingly similar error comes up;
(...) mri_convert rh.template_areas.mgz AU_areas_template_rh.nii.gz mri_convert.bin rh.template_areas.mgz AU_areas_template_rh.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from rh.template_areas.mgz... TR=0.00, 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) writing to AU_areas_template_rh.nii.gz... NIFTI FORMAT ERROR: nslices 117239 in volume exceeds 32768
I have tried to debug but failed so far. Has anyone come across a similar problem and do you have an opinion onto what might be causing this? The same adapted template's volume files work just fine.
--I am using Ubuntu 16.04& freesurfer v.6
Thank you so much! Idil
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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
you can convert the overlays directly to nifti, but they aren't surfaces - they are scalar fields over the surface (that is, they are one value/location with no neighborhood info). Not sure what Brainvoyager supports, but you could convert the surfaces to gifti
cheers Bruce
On Tue, 25 Jul 2017, Yagmur Ozdemir 19 wrote:
I am trying to export the overlays in .mgz format to Brainvoyager which recognizes nifti or its native .vmr format. However the mri_convert command gives error when I try to convert the templates. I thought if I could save the overlays directly onto the inflated surface files I could convert then visualize them in Brainvoyager, but couldn't figure that out so far. Thank you for the help!
Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Tuesday, July 25, 2017 7:47 PM To: Freesurfer support list Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
Hi Idil
I'm not sure what you mean. If you give us a better idea of your overall goal we can give you more helpful answers I expect Bruce On Tue, 25 Jul 2017, Yagmur Ozdemir 19 wrote:
Bruce,
Thank you so much for the help! I guess then the way to export these overlays to other softwares is writing them on the subject's inflated surface file.
Best, Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, July 24, 2017 10:36 PM To: Freesurfer support list Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
Hi Idil,
we only store surface overlays in .mgz not surfaces themselves. Try loading a surface (like lh.inflated) then load whatever you were looking at as an overlay on the surface cheers Bruce On Mon, 24 Jul 2017, Yagmur Ozdemir 19 wrote:
Hello freesurfer experts,
I am trying to use an occipital lobe template adapted to my data as several surface and volume files, and there seems to be a problem with the surface files. Whenever I try to open a surface overlay (in .mgz format) in freeview this error comes up;
freadFloat: fread failed freadFloat: fread failed ... [0]PETSC ERROR:
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range ...
When I try to convert this file to nifti format a seemingly similar error comes up;
(...) mri_convert rh.template_areas.mgz AU_areas_template_rh.nii.gz mri_convert.bin rh.template_areas.mgz AU_areas_template_rh.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from rh.template_areas.mgz... TR=0.00, 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) writing to AU_areas_template_rh.nii.gz... NIFTI FORMAT ERROR: nslices 117239 in volume exceeds 32768
I have tried to debug but failed so far. Has anyone come across a similar problem and do you have an opinion onto what might be causing this? The same adapted template's volume files work just fine.
--I am using Ubuntu 16.04& freesurfer v.6
Thank you so much! Idil
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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
When I do either of the conversions with mris_convert, the system gives freadFloat: fread failed / No such file or directory then a Segmentation fault error.
Best, Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Tuesday, July 25, 2017 10:21 PM To: Freesurfer support list Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
you can convert the overlays directly to nifti, but they aren't surfaces - they are scalar fields over the surface (that is, they are one value/location with no neighborhood info). Not sure what Brainvoyager supports, but you could convert the surfaces to gifti
cheers Bruce
On Tue, 25 Jul 2017, Yagmur Ozdemir 19 wrote:
I am trying to export the overlays in .mgz format to Brainvoyager which recognizes nifti or its native .vmr format. However the mri_convert command gives error when I try to convert the templates. I thought if I could save the overlays directly onto the inflated surface files I could convert then visualize them in Brainvoyager, but couldn't figure that out so far. Thank you for the help!
Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Tuesday, July 25, 2017 7:47 PM To: Freesurfer support list Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
Hi Idil
I'm not sure what you mean. If you give us a better idea of your overall goal we can give you more helpful answers I expect Bruce On Tue, 25 Jul 2017, Yagmur Ozdemir 19 wrote:
Bruce,
Thank you so much for the help! I guess then the way to export these overlays to other softwares is writing them on the subject's inflated surface file.
Best, Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, July 24, 2017 10:36 PM To: Freesurfer support list Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
Hi Idil,
we only store surface overlays in .mgz not surfaces themselves. Try loading a surface (like lh.inflated) then load whatever you were looking at as an overlay on the surface cheers Bruce On Mon, 24 Jul 2017, Yagmur Ozdemir 19 wrote:
Hello freesurfer experts,
I am trying to use an occipital lobe template adapted to my data as several surface and volume files, and there seems to be a problem with the surface files. Whenever I try to open a surface overlay (in .mgz format) in freeview this error comes up;
freadFloat: fread failed freadFloat: fread failed ... [0]PETSC ERROR:
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range ...
When I try to convert this file to nifti format a seemingly similar error comes up;
(...) mri_convert rh.template_areas.mgz AU_areas_template_rh.nii.gz mri_convert.bin rh.template_areas.mgz AU_areas_template_rh.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from rh.template_areas.mgz... TR=0.00, 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) writing to AU_areas_template_rh.nii.gz... NIFTI FORMAT ERROR: nslices 117239 in volume exceeds 32768
I have tried to debug but failed so far. Has anyone come across a similar problem and do you have an opinion onto what might be causing this? The same adapted template's volume files work just fine.
--I am using Ubuntu 16.04& freesurfer v.6
Thank you so much! Idil
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
what is your command line?
On 07/25/2017 03:52 PM, Yagmur Ozdemir 19 wrote:
When I do either of the conversions with mris_convert, the system gives freadFloat: fread failed / No such file or directory then a Segmentation fault error.
Best, Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Tuesday, July 25, 2017 10:21 PM To: Freesurfer support list Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
you can convert the overlays directly to nifti, but they aren't surfaces
- they are scalar fields over the surface (that is, they are one
value/location with no neighborhood info). Not sure what Brainvoyager supports, but you could convert the surfaces to gifti
cheers Bruce
On Tue, 25 Jul 2017, Yagmur Ozdemir 19 wrote:
I am trying to export the overlays in .mgz format to Brainvoyager which recognizes nifti or its native .vmr format. However the mri_convert command gives error when I try to convert the templates. I thought if I could save the overlays directly onto the inflated surface files I could convert then visualize them in Brainvoyager, but couldn't figure that out so far. Thank you for the help!
Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Tuesday, July 25, 2017 7:47 PM To: Freesurfer support list Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
Hi Idil
I'm not sure what you mean. If you give us a better idea of your overall goal we can give you more helpful answers I expect Bruce On Tue, 25 Jul 2017, Yagmur Ozdemir 19 wrote:
Bruce,
Thank you so much for the help! I guess then the way to export these overlays to other softwares is writing them on the subject's inflated surface file.
Best, Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, July 24, 2017 10:36 PM To: Freesurfer support list Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
Hi Idil,
we only store surface overlays in .mgz not surfaces themselves. Try loading a surface (like lh.inflated) then load whatever you were looking at as an overlay on the surface cheers Bruce On Mon, 24 Jul 2017, Yagmur Ozdemir 19 wrote:
Hello freesurfer experts,
I am trying to use an occipital lobe template adapted to my data as several surface and volume files, and there seems to be a problem with the surface files. Whenever I try to open a surface overlay (in .mgz format) in freeview this error comes up;
freadFloat: fread failed freadFloat: fread failed ... [0]PETSC ERROR:
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range ...
When I try to convert this file to nifti format a seemingly similar error comes up;
(...) mri_convert rh.template_areas.mgz AU_areas_template_rh.nii.gz mri_convert.bin rh.template_areas.mgz AU_areas_template_rh.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from rh.template_areas.mgz... TR=0.00, 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) writing to AU_areas_template_rh.nii.gz... NIFTI FORMAT ERROR: nslices 117239 in volume exceeds 32768
I have tried to debug but failed so far. Has anyone come across a similar problem and do you have an opinion onto what might be causing this? The same adapted template's volume files work just fine.
--I am using Ubuntu 16.04& freesurfer v.6
Thank you so much! Idil
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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mris_convert -c lh.template_angle.mgz lh.template_angle.mgz lh.template_angle_MW.nii
Thank you for the help, Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, July 25, 2017 11:00 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
what is your command line?
On 07/25/2017 03:52 PM, Yagmur Ozdemir 19 wrote:
When I do either of the conversions with mris_convert, the system gives freadFloat: fread failed / No such file or directory then a Segmentation fault error.
Best, Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Tuesday, July 25, 2017 10:21 PM To: Freesurfer support list Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
you can convert the overlays directly to nifti, but they aren't surfaces
- they are scalar fields over the surface (that is, they are one
value/location with no neighborhood info). Not sure what Brainvoyager supports, but you could convert the surfaces to gifti
cheers Bruce
On Tue, 25 Jul 2017, Yagmur Ozdemir 19 wrote:
I am trying to export the overlays in .mgz format to Brainvoyager which recognizes nifti or its native .vmr format. However the mri_convert command gives error when I try to convert the templates. I thought if I could save the overlays directly onto the inflated surface files I could convert then visualize them in Brainvoyager, but couldn't figure that out so far. Thank you for the help!
Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Tuesday, July 25, 2017 7:47 PM To: Freesurfer support list Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
Hi Idil
I'm not sure what you mean. If you give us a better idea of your overall goal we can give you more helpful answers I expect Bruce On Tue, 25 Jul 2017, Yagmur Ozdemir 19 wrote:
Bruce,
Thank you so much for the help! I guess then the way to export these overlays to other softwares is writing them on the subject's inflated surface file.
Best, Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, July 24, 2017 10:36 PM To: Freesurfer support list Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
Hi Idil,
we only store surface overlays in .mgz not surfaces themselves. Try loading a surface (like lh.inflated) then load whatever you were looking at as an overlay on the surface cheers Bruce On Mon, 24 Jul 2017, Yagmur Ozdemir 19 wrote:
Hello freesurfer experts,
I am trying to use an occipital lobe template adapted to my data as several surface and volume files, and there seems to be a problem with the surface files. Whenever I try to open a surface overlay (in .mgz format) in freeview this error comes up;
freadFloat: fread failed freadFloat: fread failed ... [0]PETSC ERROR:
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range ...
When I try to convert this file to nifti format a seemingly similar error comes up;
(...) mri_convert rh.template_areas.mgz AU_areas_template_rh.nii.gz mri_convert.bin rh.template_areas.mgz AU_areas_template_rh.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from rh.template_areas.mgz... TR=0.00, 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) writing to AU_areas_template_rh.nii.gz... NIFTI FORMAT ERROR: nslices 117239 in volume exceeds 32768
I have tried to debug but failed so far. Has anyone come across a similar problem and do you have an opinion onto what might be causing this? The same adapted template's volume files work just fine.
--I am using Ubuntu 16.04& freesurfer v.6
Thank you so much! Idil
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
you can just
mri_convert lh.template_angle.mgz lh.template_angle_MW.nii
not, mri_convert, not mris_convert
On 07/25/2017 04:16 PM, Yagmur Ozdemir 19 wrote:
mris_convert -c lh.template_angle.mgz lh.template_angle.mgz lh.template_angle_MW.nii
Thank you for the help, Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, July 25, 2017 11:00 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
what is your command line?
On 07/25/2017 03:52 PM, Yagmur Ozdemir 19 wrote:
When I do either of the conversions with mris_convert, the system gives freadFloat: fread failed / No such file or directory then a Segmentation fault error.
Best, Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Tuesday, July 25, 2017 10:21 PM To: Freesurfer support list Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
you can convert the overlays directly to nifti, but they aren't surfaces
- they are scalar fields over the surface (that is, they are one
value/location with no neighborhood info). Not sure what Brainvoyager supports, but you could convert the surfaces to gifti
cheers Bruce
On Tue, 25 Jul 2017, Yagmur Ozdemir 19 wrote:
I am trying to export the overlays in .mgz format to Brainvoyager which recognizes nifti or its native .vmr format. However the mri_convert command gives error when I try to convert the templates. I thought if I could save the overlays directly onto the inflated surface files I could convert then visualize them in Brainvoyager, but couldn't figure that out so far. Thank you for the help!
Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Tuesday, July 25, 2017 7:47 PM To: Freesurfer support list Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
Hi Idil
I'm not sure what you mean. If you give us a better idea of your overall goal we can give you more helpful answers I expect Bruce On Tue, 25 Jul 2017, Yagmur Ozdemir 19 wrote:
Bruce,
Thank you so much for the help! I guess then the way to export these overlays to other softwares is writing them on the subject's inflated surface file.
Best, Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, July 24, 2017 10:36 PM To: Freesurfer support list Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
Hi Idil,
we only store surface overlays in .mgz not surfaces themselves. Try loading a surface (like lh.inflated) then load whatever you were looking at as an overlay on the surface cheers Bruce On Mon, 24 Jul 2017, Yagmur Ozdemir 19 wrote:
Hello freesurfer experts,
I am trying to use an occipital lobe template adapted to my data as several surface and volume files, and there seems to be a problem with the surface files. Whenever I try to open a surface overlay (in .mgz format) in freeview this error comes up;
freadFloat: fread failed freadFloat: fread failed ... [0]PETSC ERROR:
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range ...
When I try to convert this file to nifti format a seemingly similar error comes up;
(...) mri_convert rh.template_areas.mgz AU_areas_template_rh.nii.gz mri_convert.bin rh.template_areas.mgz AU_areas_template_rh.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from rh.template_areas.mgz... TR=0.00, 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) writing to AU_areas_template_rh.nii.gz... NIFTI FORMAT ERROR: nslices 117239 in volume exceeds 32768
I have tried to debug but failed so far. Has anyone come across a similar problem and do you have an opinion onto what might be causing this? The same adapted template's volume files work just fine.
--I am using Ubuntu 16.04& freesurfer v.6
Thank you so much! Idil
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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
I just realized I needed lh.inflated in the command. I think it works now. Thank you for all the help!
Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, July 25, 2017 11:00 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
what is your command line?
On 07/25/2017 03:52 PM, Yagmur Ozdemir 19 wrote:
When I do either of the conversions with mris_convert, the system gives freadFloat: fread failed / No such file or directory then a Segmentation fault error.
Best, Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Tuesday, July 25, 2017 10:21 PM To: Freesurfer support list Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
you can convert the overlays directly to nifti, but they aren't surfaces
- they are scalar fields over the surface (that is, they are one
value/location with no neighborhood info). Not sure what Brainvoyager supports, but you could convert the surfaces to gifti
cheers Bruce
On Tue, 25 Jul 2017, Yagmur Ozdemir 19 wrote:
I am trying to export the overlays in .mgz format to Brainvoyager which recognizes nifti or its native .vmr format. However the mri_convert command gives error when I try to convert the templates. I thought if I could save the overlays directly onto the inflated surface files I could convert then visualize them in Brainvoyager, but couldn't figure that out so far. Thank you for the help!
Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Tuesday, July 25, 2017 7:47 PM To: Freesurfer support list Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
Hi Idil
I'm not sure what you mean. If you give us a better idea of your overall goal we can give you more helpful answers I expect Bruce On Tue, 25 Jul 2017, Yagmur Ozdemir 19 wrote:
Bruce,
Thank you so much for the help! I guess then the way to export these overlays to other softwares is writing them on the subject's inflated surface file.
Best, Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, July 24, 2017 10:36 PM To: Freesurfer support list Subject: Re: [Freesurfer] Segmentation Violation problem in surface files
Hi Idil,
we only store surface overlays in .mgz not surfaces themselves. Try loading a surface (like lh.inflated) then load whatever you were looking at as an overlay on the surface cheers Bruce On Mon, 24 Jul 2017, Yagmur Ozdemir 19 wrote:
Hello freesurfer experts,
I am trying to use an occipital lobe template adapted to my data as several surface and volume files, and there seems to be a problem with the surface files. Whenever I try to open a surface overlay (in .mgz format) in freeview this error comes up;
freadFloat: fread failed freadFloat: fread failed ... [0]PETSC ERROR:
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range ...
When I try to convert this file to nifti format a seemingly similar error comes up;
(...) mri_convert rh.template_areas.mgz AU_areas_template_rh.nii.gz mri_convert.bin rh.template_areas.mgz AU_areas_template_rh.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from rh.template_areas.mgz... TR=0.00, 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) writing to AU_areas_template_rh.nii.gz... NIFTI FORMAT ERROR: nslices 117239 in volume exceeds 32768
I have tried to debug but failed so far. Has anyone come across a similar problem and do you have an opinion onto what might be causing this? The same adapted template's volume files work just fine.
--I am using Ubuntu 16.04& freesurfer v.6
Thank you so much! Idil
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas N Greve -
Yagmur Ozdemir 19