External Email - Use Caution
Hello.
I manually edited the brainmask.mgz file for three subjects. This was done to prevent the pial surface from extending into non-cortical areas, in particular the soft-tissue near the brain stem, and some cerebellar areas. Usually this type of editing (just removing voxels from brianmask.mgz) doesn't give me any trouble, and I use the command recon-all -make all -subjid <subject_id> -sd <subject_dir> to then rebuild the surfaces.
However, the tail of the log shows that the pipeline exited with errors, with a few commands near the end related to curvstats and jacobian_white failing. The new surfaces seem to look fine in freeview. The edits to brainmask were registered correctly, but I'm still concerned that the errors might affect an mri_glmfit analysis. This is true for all three subjects I edited, which seems odd, and I'm not sure what would be causing this.
Below is a pastebin showing the relevant errors. The rest of the pipeline seems to execute without errors. I could send entire log if necessary.
https://pastebin.com/b4JX04AThttps://pastebin.com/raw/b4JX04AT
Thanks,
- Eli
Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient care. Houston Methodist is nationally ranked in 8 specialties and is designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.
Hi Eli
yes, please send the recon-all.log
thanks Bruce On Mon, 30 Jul 2018, Rockers, Elijah D. wrote:
External Email - Use Caution
Hello.
I manually edited the brainmask.mgz file for three subjects. This was done to prevent the pial surface from extending into non-cortical areas, in particular the soft-tissue near the brain stem, and some cerebellar areas. Usually this type of editing (just removing voxels from brianmask.mgz) doesn't give me any trouble, and I use the command recon-all -make all -subjid <subject_id> -sd <subject_dir> to then rebuild the surfaces.
However, the tail of the log shows that the pipeline exited with errors, with a few commands near the end related to curvstats and jacobian_white failing. The new surfaces seem to look fine in freeview. The edits to brainmask were registered correctly, but I'm still concerned that the errors might affect an mri_glmfit analysis. This is true for all three subjects I edited, which seems odd, and I'm not sure what would be causing this.
Below is a pastebin showing the relevant errors. The rest of the pipeline seems to execute without errors. I could send entire log if necessary.
https://pastebin.com/raw/b4JX04AT
Thanks,
- Eli
Houston Methodist. Leading Medicine.
Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient care. Houston Methodist is nationally ranked in 8 specialties and is designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist.
***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Rockers, Elijah D.