Hello Freesurfer List Gurus,
We're at the stage of making white matter edits and adding control points, but one of my subjects recently produced the following error:
zcat: /study/midus/data/mri/processed/freesurfer/subject057/mri/wm.seg.mgz: unexpected end of file mghRead(/study/midus/data/mri/processed/freesurfer/subject057/mri/wm.seg.mgz): could not read 65536 bytes at slice 90 mri_segment: could not read file wm.seg.mgz to preserve edits Linux cashew.keck.waisman.wisc.edu 2.6.18-164.6.1.el5 #1 SMP Tue Nov 3 23:11:58 EST 2009 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Tue May 18 21:04:35 CDT 2010
Any suggestions on how to fix? This subject has already had a great deal of hands on processing in terms of adding control points, editing the white matter, and running recon_all to fix, with multiple passes to get it as perfect as possible. Also, I've TRIED just rerunning recon-all on it, but the errors persist. (Each time, we're running the following command: recon-all -autorecon2-cp -autorecon3 -subjid subject057)
Any and all info on how to salvage this subject's data without have to start from scratch will be much appreciated!
Thank you. Stacey Schaefer
--------------------------------------------------- Stacey M. Schaefer, Ph.D. Waisman Laboratory for Brain Imaging and Behavior University of Wisconsin - Madison 1500 Highland Ave Rm T127 Madison, WI 53705 Waisman Phone: 608-263-9321 Laboratory for Affective Neuroscience UW Psychology Dept, Brogden 1202 W Johnson St Rm 392 Madison, WI 53706 Brogden Phone: 608-262-9937
Hi Stacey,
usually that means the partition is full. Can you check it with df?
cheers Bruce
On Sat, 22 May 2010, Stacey M Schaefer wrote:
Hello Freesurfer List Gurus,
We're at the stage of making white matter edits and adding control points, but one of my subjects recently produced the following error:
zcat: /study/midus/data/mri/processed/freesurfer/subject057/mri/wm.seg.mgz: unexpected end of file mghRead(/study/midus/data/mri/processed/freesurfer/subject057/mri/wm.seg.mgz): could not read 65536 bytes at slice 90 mri_segment: could not read file wm.seg.mgz to preserve edits Linux cashew.keck.waisman.wisc.edu 2.6.18-164.6.1.el5 #1 SMP Tue Nov 3 23:11:58 EST 2009 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Tue May 18 21:04:35 CDT 2010
Any suggestions on how to fix? This subject has already had a great deal of hands on processing in terms of adding control points, editing the white matter, and running recon_all to fix, with multiple passes to get it as perfect as possible. Also, I've TRIED just rerunning recon-all on it, but the errors persist. (Each time, we're running the following command: recon-all -autorecon2-cp -autorecon3 -subjid subject057)
Any and all info on how to salvage this subject's data without have to start from scratch will be much appreciated!
Thank you. Stacey Schaefer
Stacey M. Schaefer, Ph.D. Waisman Laboratory for Brain Imaging and Behavior University of Wisconsin - Madison 1500 Highland Ave Rm T127 Madison, WI 53705 Waisman Phone: 608-263-9321 Laboratory for Affective Neuroscience UW Psychology Dept, Brogden 1202 W Johnson St Rm 392 Madison, WI 53706 Brogden Phone: 608-262-9937 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Bruce,
There is room currently on the drive, although it might have filled up in an earlier run of recon_all (many people/studies share the same drive space and we ran into space issues a week back). If the wm.seg.mgz file was corrupted at that point, is there a way I can regenerate it without losing all of the hand edits we've made already?
Thanks very much for your help! Stacey
--------------------------------------------------- Stacey M. Schaefer, Ph.D. Waisman Laboratory for Brain Imaging and Behavior University of Wisconsin - Madison 1500 Highland Ave Rm T127 Madison, WI 53705 Waisman Phone: 608-263-9321 Laboratory for Affective Neuroscience UW Psychology Dept, Brogden 1202 W Johnson St Rm 392 Madison, WI 53706 Brogden Phone: 608-262-9937
----- Original Message ----- From: Bruce Fischl fischl@nmr.mgh.harvard.edu Date: Saturday, May 22, 2010 1:17 pm Subject: Re: [Freesurfer] recon-all ERROR reading wm.seg.mgz when doing routine correction processing To: Stacey M Schaefer smschaefer2@wisc.edu Cc: freesurfer@nmr.mgh.harvard.edu
Hi Stacey,
usually that means the partition is full. Can you check it with df?
cheers Bruce
On Sat, 22 May 2010, Stacey M Schaefer wrote:
Hello Freesurfer List Gurus,
We're at the stage of making white matter edits and adding control
points, but one of my subjects recently produced the following error:
zcat:
/study/midus/data/mri/processed/freesurfer/subject057/mri/wm.seg.mgz: unexpected end of file
mghRead(/study/midus/data/mri/processed/freesurfer/subject057/mri/wm.seg.mgz):
could not read 65536 bytes at slice 90
mri_segment: could not read file wm.seg.mgz to preserve edits Linux cashew.keck.waisman.wisc.edu 2.6.18-164.6.1.el5 #1 SMP Tue Nov
3 23:11:58 EST 2009 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Tue May 18 21:04:35 CDT 2010
Any suggestions on how to fix? This subject has already had a great
deal of hands on processing in terms of adding control points, editing the white matter, and running recon_all to fix, with multiple passes to get it as perfect as possible. Also, I've TRIED just rerunning recon-all on it, but the errors persist. (Each time, we're running the following command:
recon-all -autorecon2-cp -autorecon3 -subjid subject057)
Any and all info on how to salvage this subject's data without have
to start from scratch will be much appreciated!
Thank you. Stacey Schaefer
Stacey M. Schaefer, Ph.D. Waisman Laboratory for Brain Imaging and Behavior University of Wisconsin - Madison 1500 Highland Ave Rm T127 Madison, WI 53705 Waisman Phone: 608-263-9321 Laboratory for Affective Neuroscience UW Psychology Dept, Brogden 1202 W Johnson St Rm 392 Madison, WI 53706 Brogden Phone: 608-262-9937 _______________________________________________ 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 Stacey,
if the file didn't get completely written it won't be easy. I guess you could try loading what is there in matlab and copying over the voxels that have edits in them, but our I/O won't work since it isn't the right size. You would need to write youw own. Probably just easier to re-edit I would think
Bruce
On Mon, 24 May 2010, Stacey M Schaefer wrote:
Hello Bruce,
There is room currently on the drive, although it might have filled up in an earlier run of recon_all (many people/studies share the same drive space and we ran into space issues a week back). If the wm.seg.mgz file was corrupted at that point, is there a way I can regenerate it without losing all of the hand edits we've made already?
Thanks very much for your help! Stacey
Stacey M. Schaefer, Ph.D. Waisman Laboratory for Brain Imaging and Behavior University of Wisconsin - Madison 1500 Highland Ave Rm T127 Madison, WI 53705 Waisman Phone: 608-263-9321 Laboratory for Affective Neuroscience UW Psychology Dept, Brogden 1202 W Johnson St Rm 392 Madison, WI 53706 Brogden Phone: 608-262-9937
----- Original Message ----- From: Bruce Fischl fischl@nmr.mgh.harvard.edu Date: Saturday, May 22, 2010 1:17 pm Subject: Re: [Freesurfer] recon-all ERROR reading wm.seg.mgz when doing routine correction processing To: Stacey M Schaefer smschaefer2@wisc.edu Cc: freesurfer@nmr.mgh.harvard.edu
Hi Stacey,
usually that means the partition is full. Can you check it with df?
cheers Bruce
On Sat, 22 May 2010, Stacey M Schaefer wrote:
Hello Freesurfer List Gurus,
We're at the stage of making white matter edits and adding control
points, but one of my subjects recently produced the following error:
zcat:
/study/midus/data/mri/processed/freesurfer/subject057/mri/wm.seg.mgz: unexpected end of file
mghRead(/study/midus/data/mri/processed/freesurfer/subject057/mri/wm.seg.mgz):
could not read 65536 bytes at slice 90
mri_segment: could not read file wm.seg.mgz to preserve edits Linux cashew.keck.waisman.wisc.edu 2.6.18-164.6.1.el5 #1 SMP Tue Nov
3 23:11:58 EST 2009 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Tue May 18 21:04:35 CDT 2010
Any suggestions on how to fix? This subject has already had a great
deal of hands on processing in terms of adding control points, editing the white matter, and running recon_all to fix, with multiple passes to get it as perfect as possible. Also, I've TRIED just rerunning recon-all on it, but the errors persist. (Each time, we're running the following command:
recon-all -autorecon2-cp -autorecon3 -subjid subject057)
Any and all info on how to salvage this subject's data without have
to start from scratch will be much appreciated!
Thank you. Stacey Schaefer
Stacey M. Schaefer, Ph.D. Waisman Laboratory for Brain Imaging and Behavior University of Wisconsin - Madison 1500 Highland Ave Rm T127 Madison, WI 53705 Waisman Phone: 608-263-9321 Laboratory for Affective Neuroscience UW Psychology Dept, Brogden 1202 W Johnson St Rm 392 Madison, WI 53706 Brogden Phone: 608-262-9937 _______________________________________________ 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 -
Stacey M Schaefer