Dear FreeSurfer Experts,
I’m recently getting an error in make_average_subject and can’t find the reason.
Please see the following for the error log from recon-all.log:
mri_aparc2aseg --s avgsubject1 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /home/lakshman/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt
relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /home/lakshman/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /home/lakshman/freesurfer/subjects subject avgsubject1 outvol /home/lakshman/freesurfer/subjects/avgsubject1/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0
Reading lh white surface /home/lakshman/freesurfer/subjects/avgsubject1/surf/lh.white
Reading lh pial surface /home/lakshman/freesurfer/subjects/avgsubject1/surf/lh.pial
Loading lh annotations from /home/lakshman/freesurfer/subjects/avgsubject1/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /home/lakshman/freesurfer/subjects/avgsubject1/label/tmpdir.annot2std.30180/seg.1.MRI-98004548-1c415d596e6fc5f9.ctab)
Reading rh white surface /home/lakshman/freesurfer/subjects/avgsubject1/surf/rh.white
Reading rh pial surface /home/lakshman/freesurfer/subjects/avgsubject1/surf/rh.pial
Loading rh annotations from /home/lakshman/freesurfer/subjects/avgsubject1/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /home/lakshman/freesurfer/subjects/avgsubject1/label/tmpdir.annot2std.33768/seg.1.MRI-98004548-1c415d596e6fc5f9.ctab) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /home/lakshman/freesurfer/subjects/avgsubject1/mri/ribbon.mgz
Building hash of lh white
Building hash of lh pial
Building hash of rh white
Building hash of rh pial
Loading aseg from /home/lakshman/freesurfer/subjects/avgsubject1/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; mghRead(mri/norm.mgz, -1): could not open file -------------------------
Labeling Slice relabeling unlikely voxels in interior of white matter mri/norm.mgz: could not load norm volume from
Could you please help us in resolving the issue.
Have also attached the recon-all log for reference.
Thanks & Regards, Janani
::DISCLAIMER:: -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects. --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Hi Janani,
We have a patch for this bug here: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/
The second part of the readme file in that directory provides instructions for resolving this.
best Andrew
On February 19, 2018 at 9:40:22 AM, M Janani (jananimj@hcl.commailto:jananimj@hcl.com) wrote:
Dear FreeSurfer Experts,
I’m recently getting an error in make_average_subject and can’t find the reason.
Please see the following for the error log from recon-all.log:
mri_aparc2aseg --s avgsubject1 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /home/lakshman/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt
relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /home/lakshman/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /home/lakshman/freesurfer/subjects subject avgsubject1 outvol /home/lakshman/freesurfer/subjects/avgsubject1/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0
Reading lh white surface /home/lakshman/freesurfer/subjects/avgsubject1/surf/lh.white
Reading lh pial surface /home/lakshman/freesurfer/subjects/avgsubject1/surf/lh.pial
Loading lh annotations from /home/lakshman/freesurfer/subjects/avgsubject1/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /home/lakshman/freesurfer/subjects/avgsubject1/label/tmpdir.annot2std.30180/seg.1.MRI-98004548-1c415d596e6fc5f9.ctab)
Reading rh white surface /home/lakshman/freesurfer/subjects/avgsubject1/surf/rh.white
Reading rh pial surface /home/lakshman/freesurfer/subjects/avgsubject1/surf/rh.pial
Loading rh annotations from /home/lakshman/freesurfer/subjects/avgsubject1/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /home/lakshman/freesurfer/subjects/avgsubject1/label/tmpdir.annot2std.33768/seg.1.MRI-98004548-1c415d596e6fc5f9.ctab) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /home/lakshman/freesurfer/subjects/avgsubject1/mri/ribbon.mgz
Building hash of lh white
Building hash of lh pial
Building hash of rh white
Building hash of rh pial
Loading aseg from /home/lakshman/freesurfer/subjects/avgsubject1/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; mghRead(mri/norm.mgz, -1): could not open file -------------------------
Labeling Slice relabeling unlikely voxels in interior of white matter mri/norm.mgz: could not load norm volume from
Could you please help us in resolving the issue.
Have also attached the recon-all log for reference.
Thanks & Regards, Janani
::DISCLAIMER:: -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects. -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hey Andrew,
I am running FreeSurfer 6.0 on MacOS X and ran into the exact same issue as Janani, so I installed this patch. However, now I am getting the following error:
#@# AParc-to-ASeg aparc Tue Feb 20 11:04:08 EST 2018
/Users/scottpruett/Desktop/CSMRI/Freesurfer/601_10y_av
\n mri_aparc2aseg --s 601_10y_av --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /Applications/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --no-relabel \n
/Applications/freesurfer/bin/mri_aparc2aseg: Exec format error. Binary file not executable.
Darwin scott-pruetts-computer.local 17.3.0 Darwin Kernel Version 17.3.0: Thu Nov 9 18:09:22 PST 2017; root:xnu-4570.31.3~1/RELEASE_X86_64 x86_64
recon-all -s 601_10y_av exited with ERRORS at Tue Feb 20 11:04:10 EST 2018
I've attached the recon-all.log file. Any help would be greatly appreciated.
Best,
Scott
On Tue, Feb 20, 2018 at 10:25 AM, Hoopes, Andrew AHOOPES@mgh.harvard.edu wrote:
Hi Janani,
We have a patch for this bug here: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/
The second part of the readme file in that directory provides instructions for resolving this.
best Andrew
On February 19, 2018 at 9:40:22 AM, M Janani (jananimj@hcl.com) wrote:
Dear FreeSurfer Experts,
I’m recently getting an error in make_average_subject and can’t find the reason. Please see the following for the error log from recon-all.log: mri_aparc2aseg --s avgsubject1 --volmask --aseg aseg.presurf.hypos--relabel mri/norm.mgz mri/transforms/talairach.m3z /home/lakshman/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt
relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /home/lakshman/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /home/lakshman/freesurfer/subjects subject avgsubject1 outvol /home/lakshman/freesurfer/subjects/avgsubject1/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0
Reading lh white surface /home/lakshman/freesurfer/subjects/avgsubject1/surf/lh.white
Reading lh pial surface /home/lakshman/freesurfer/subjects/avgsubject1/surf/lh.pial
Loading lh annotations from /home/lakshman/freesurfer/ subjects/avgsubject1/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /home/lakshman/freesurfer/ subjects/avgsubject1/label/tmpdir.annot2std.30180/seg.1. MRI-98004548-1c415d596e6fc5f9.ctab)
Reading rh white surface /home/lakshman/freesurfer/subjects/avgsubject1/surf/rh.white
Reading rh pial surface /home/lakshman/freesurfer/subjects/avgsubject1/surf/rh.pial
Loading rh annotations from /home/lakshman/freesurfer/ subjects/avgsubject1/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /home/lakshman/freesurfer/ subjects/avgsubject1/label/tmpdir.annot2std.33768/seg.1. MRI-98004548-1c415d596e6fc5f9.ctab) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /home/lakshman/freesurfer/ subjects/avgsubject1/mri/ribbon.mgz
Building hash of lh white
Building hash of lh pial
Building hash of rh white
Building hash of rh pial
Loading aseg from /home/lakshman/freesurfer/subjects/avgsubject1/mri/aseg. presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; mghRead(mri/norm.mgz, -1): could not open file
Labeling Slice relabeling unlikely voxels in interior of white matter *mri/norm.mgz: could not load norm volume from *
Could you please help us in resolving the issue.
Have also attached the recon-all log for reference.
Thanks & Regards, Janani
::DISCLAIMER::
The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects.
-------------------------------------- _______________________________________________
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
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 Scott,
It looks like the mri_aparc2aseg binary in that patch directory was compiled for centos. The version at the following link was compiled on OS X: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/OSX-ElCa...
If you download this new mri_aparc2aseg into your $FREESURFER_HOME/bin, it should fix the issue.
best Andrew
On February 20, 2018 at 11:22:20 AM, Pruett, Scott (brandon_pruett@brown.edumailto:brandon_pruett@brown.edu) wrote:
Hey Andrew,
I am running FreeSurfer 6.0 on MacOS X and ran into the exact same issue as Janani, so I installed this patch. However, now I am getting the following error:
#@# AParc-to-ASeg aparc Tue Feb 20 11:04:08 EST 2018
/Users/scottpruett/Desktop/CSMRI/Freesurfer/601_10y_av
\n mri_aparc2aseg --s 601_10y_av --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /Applications/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --no-relabel \n
/Applications/freesurfer/bin/mri_aparc2aseg: Exec format error. Binary file not executable.
Darwin scott-pruetts-computer.local 17.3.0 Darwin Kernel Version 17.3.0: Thu Nov 9 18:09:22 PST 2017; root:xnu-4570.31.3~1/RELEASE_X86_64 x86_64
recon-all -s 601_10y_av exited with ERRORS at Tue Feb 20 11:04:10 EST 2018
I've attached the recon-all.log file. Any help would be greatly appreciated.
Best,
Scott
On Tue, Feb 20, 2018 at 10:25 AM, Hoopes, Andrew <AHOOPES@mgh.harvard.edumailto:AHOOPES@mgh.harvard.edu> wrote: Hi Janani,
We have a patch for this bug here: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/
The second part of the readme file in that directory provides instructions for resolving this.
best Andrew
On February 19, 2018 at 9:40:22 AM, M Janani (jananimj@hcl.commailto:jananimj@hcl.com) wrote:
Dear FreeSurfer Experts,
I’m recently getting an error in make_average_subject and can’t find the reason.
Please see the following for the error log from recon-all.log:
mri_aparc2aseg --s avgsubject1 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /home/lakshman/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt
relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /home/lakshman/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /home/lakshman/freesurfer/subjects subject avgsubject1 outvol /home/lakshman/freesurfer/subjects/avgsubject1/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0
Reading lh white surface /home/lakshman/freesurfer/subjects/avgsubject1/surf/lh.white
Reading lh pial surface /home/lakshman/freesurfer/subjects/avgsubject1/surf/lh.pial
Loading lh annotations from /home/lakshman/freesurfer/subjects/avgsubject1/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /home/lakshman/freesurfer/subjects/avgsubject1/label/tmpdir.annot2std.30180/seg.1.MRI-98004548-1c415d596e6fc5f9.ctab)
Reading rh white surface /home/lakshman/freesurfer/subjects/avgsubject1/surf/rh.white
Reading rh pial surface /home/lakshman/freesurfer/subjects/avgsubject1/surf/rh.pial
Loading rh annotations from /home/lakshman/freesurfer/subjects/avgsubject1/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /home/lakshman/freesurfer/subjects/avgsubject1/label/tmpdir.annot2std.33768/seg.1.MRI-98004548-1c415d596e6fc5f9.ctab) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /home/lakshman/freesurfer/subjects/avgsubject1/mri/ribbon.mgz
Building hash of lh white
Building hash of lh pial
Building hash of rh white
Building hash of rh pial
Loading aseg from /home/lakshman/freesurfer/subjects/avgsubject1/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; mghRead(mri/norm.mgz, -1): could not open file -------------------------
Labeling Slice relabeling unlikely voxels in interior of white matter mri/norm.mgz: could not load norm volume from
Could you please help us in resolving the issue.
Have also attached the recon-all log for reference.
Thanks & Regards, Janani
::DISCLAIMER:: -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects. -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
-- Scott Pruett, M.D., Ph.D. General Psychiatry and R25 Research Track Resident, PGY4 Department of Psychiatry and Human Behavior Warren Alpert Medical School of Brown University _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks, Andrew!
On Tue, Feb 20, 2018 at 11:42 AM, Hoopes, Andrew AHOOPES@mgh.harvard.edu wrote:
Hi Scott,
It looks like the mri_aparc2aseg binary in that patch directory was compiled for centos. The version at the following link was compiled on OS X: https://surfer.nmr.mgh.harvard.edu/pub/dist/ freesurfer/dev_binaries/OSX-ElCapitan/mri_aparc2aseg
If you download this new mri_aparc2aseg into your $FREESURFER_HOME/bin, it should fix the issue.
best Andrew
On February 20, 2018 at 11:22:20 AM, Pruett, Scott ( brandon_pruett@brown.edu) wrote:
Hey Andrew,
I am running FreeSurfer 6.0 on MacOS X and ran into the exact same issue as Janani, so I installed this patch. However, now I am getting the following error:
#@# AParc-to-ASeg aparc Tue Feb 20 11:04:08 EST 2018
/Users/scottpruett/Desktop/CSMRI/Freesurfer/601_10y_av
\n mri_aparc2aseg --s 601_10y_av --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /Applications/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --no-relabel \n
/Applications/freesurfer/bin/mri_aparc2aseg: Exec format error. Binary file not executable.
Darwin scott-pruetts-computer.local 17.3.0 Darwin Kernel Version 17.3.0: Thu Nov 9 18:09:22 PST 2017; root:xnu-4570.31.3~1/RELEASE_X86_64 x86_64
recon-all -s 601_10y_av exited with ERRORS at Tue Feb 20 11:04:10 EST 2018
I've attached the recon-all.log file. Any help would be greatly appreciated.
Best,
Scott
On Tue, Feb 20, 2018 at 10:25 AM, Hoopes, Andrew AHOOPES@mgh.harvard.edu wrote:
Hi Janani,
We have a patch for this bug here: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/
The second part of the readme file in that directory provides instructions for resolving this.
best Andrew
On February 19, 2018 at 9:40:22 AM, M Janani (jananimj@hcl.com) wrote:
Dear FreeSurfer Experts,
I’m recently getting an error in make_average_subject and can’t find the reason. Please see the following for the error log from recon-all.log: mri_aparc2aseg --s avgsubject1 --volmask --asegaseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /home/lakshman/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt
relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /home/lakshman/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /home/lakshman/freesurfer/subjects subject avgsubject1 outvol /home/lakshman/freesurfer/subjects/avgsubject1/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0
Reading lh white surface /home/lakshman/freesurfer/subjects/avgsubject1/surf/lh.white
Reading lh pial surface /home/lakshman/freesurfer/subjects/avgsubject1/surf/lh.pial
Loading lh annotations from /home/lakshman/freesurfer/subj ects/avgsubject1/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /home/lakshman/freesurfer/subj ects/avgsubject1/label/tmpdir.annot2std.30180/seg.1.MRI- 98004548-1c415d596e6fc5f9.ctab)
Reading rh white surface /home/lakshman/freesurfer/subjects/avgsubject1/surf/rh.white
Reading rh pial surface /home/lakshman/freesurfer/subjects/avgsubject1/surf/rh.pial
Loading rh annotations from /home/lakshman/freesurfer/subj ects/avgsubject1/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /home/lakshman/freesurfer/subj ects/avgsubject1/label/tmpdir.annot2std.33768/seg.1.MRI- 98004548-1c415d596e6fc5f9.ctab) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /home/lakshman/freesurfer/subj ects/avgsubject1/mri/ribbon.mgz
Building hash of lh white
Building hash of lh pial
Building hash of rh white
Building hash of rh pial
Loading aseg from /home/lakshman/freesurfer/subj ects/avgsubject1/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; mghRead(mri/norm.mgz, -1): could not open file
Labeling Slice relabeling unlikely voxels in interior of white matter *mri/norm.mgz: could not load norm volume from *
Could you please help us in resolving the issue.
Have also attached the recon-all log for reference.
Thanks & Regards, Janani
::DISCLAIMER::
The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects.
-------------------------------------- ______________________________ _________________ 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
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.
-- Scott Pruett, M.D., Ph.D. General Psychiatry and R25 Research Track Resident, PGY4 Department of Psychiatry and Human Behavior Warren Alpert Medical School of Brown University _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks andrew... I will try this ________________________________ From: Hoopes, Andrew AHOOPES@mgh.harvard.edu Sent: Tuesday, February 20, 2018 8:55:47 PM To: M Janani; Freesurfer support list Cc: Sasikala Sethu Subject: Re: [Freesurfer] Error in running make_average_subject
Hi Janani,
We have a patch for this bug here: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/
The second part of the readme file in that directory provides instructions for resolving this.
best Andrew
On February 19, 2018 at 9:40:22 AM, M Janani (jananimj@hcl.commailto:jananimj@hcl.com) wrote:
Dear FreeSurfer Experts,
I’m recently getting an error in make_average_subject and can’t find the reason.
Please see the following for the error log from recon-all.log:
mri_aparc2aseg --s avgsubject1 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /home/lakshman/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt
relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /home/lakshman/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /home/lakshman/freesurfer/subjects subject avgsubject1 outvol /home/lakshman/freesurfer/subjects/avgsubject1/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0
Reading lh white surface /home/lakshman/freesurfer/subjects/avgsubject1/surf/lh.white
Reading lh pial surface /home/lakshman/freesurfer/subjects/avgsubject1/surf/lh.pial
Loading lh annotations from /home/lakshman/freesurfer/subjects/avgsubject1/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /home/lakshman/freesurfer/subjects/avgsubject1/label/tmpdir.annot2std.30180/seg.1.MRI-98004548-1c415d596e6fc5f9.ctab)
Reading rh white surface /home/lakshman/freesurfer/subjects/avgsubject1/surf/rh.white
Reading rh pial surface /home/lakshman/freesurfer/subjects/avgsubject1/surf/rh.pial
Loading rh annotations from /home/lakshman/freesurfer/subjects/avgsubject1/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /home/lakshman/freesurfer/subjects/avgsubject1/label/tmpdir.annot2std.33768/seg.1.MRI-98004548-1c415d596e6fc5f9.ctab) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /home/lakshman/freesurfer/subjects/avgsubject1/mri/ribbon.mgz
Building hash of lh white
Building hash of lh pial
Building hash of rh white
Building hash of rh pial
Loading aseg from /home/lakshman/freesurfer/subjects/avgsubject1/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; mghRead(mri/norm.mgz, -1): could not open file -------------------------
Labeling Slice relabeling unlikely voxels in interior of white matter mri/norm.mgz: could not load norm volume from
Could you please help us in resolving the issue.
Have also attached the recon-all log for reference.
Thanks & Regards, Janani
::DISCLAIMER:: -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects. -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- _______________________________________________ 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
-
Hoopes, Andrew -
M Janani -
Pruett, Scott