Re: [Freesurfer] Disastrous Soft Error
Glad to hear it worked out Bruce > On Feb 24, 2017, at 5:01 PM, Rockers, Elijah D. > wrote: > > OK, sorry for spamming the list. I fixed the the faulty skullstrip by using > > recon-all -skullstrip -clean-bm -no-wsgcaatlas -subjid > > Currently redoing the surface reconstructions, but it should be OK now. > Thanks for the nice documentation. > Eli > > >> On Fri, 2017-02-24 at 15:30 -0600, Elijah Rockers wrote: >> As far as I can tell, everything looks OK up until brainmask.mgz. The >> skullstrip step seems to have cropped out the brain and left the neck... >> >> On Fri, 2017-02-24 at 12:58 -0600, Elijah Rockers wrote: >> > Hello all, >> > >> > I recon-all'd ~40 different subjects. I have been going through all the >> > images to make sure they were processed correctly. Most required no no >> > editing and recon-all did a very good job. >> > >> > But for one scan in particular, it looks like Freesurfer thinks the top >> > of the spinal cord is the brain. Several vertebrae are very nicely >> > segmented... :P >> > >> > Just wondering if you have any suggestions for reprocessing this >> > subject? The error is reproducible with default recon-all settings. >> > >> > Subject has some pathology in the white matter which might be causing >> > the problem? >> > >> > Screenshot of T1.mgz + lh.pial at the following link: >> > http://imgur.com/a/uwyaq >> > >> > Thanks, >> > Eli >> > > Houston Methodist. Leading Medicine. > > U.S. News & World Report has recognized Houston Methodist as one of the > nation’s top 20 hospitals, placing it for the second time on the magazine’s > prestigious Honor Roll. It is also 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 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.
Re: [Freesurfer] Disastrous Soft Error
OK, sorry for spamming the list. I fixed the the faulty skullstrip by using recon-all -skullstrip -clean-bm -no-wsgcaatlas -subjid Currently redoing the surface reconstructions, but it should be OK now. Thanks for the nice documentation. Eli On Fri, 2017-02-24 at 15:30 -0600, Elijah Rockers wrote: As far as I can tell, everything looks OK up until brainmask.mgz. The skullstrip step seems to have cropped out the brain and left the neck... On Fri, 2017-02-24 at 12:58 -0600, Elijah Rockers wrote: > Hello all, > > I recon-all'd ~40 different subjects. I have been going through all the > images to make sure they were processed correctly. Most required no no > editing and recon-all did a very good job. > > But for one scan in particular, it looks like Freesurfer thinks the top > of the spinal cord is the brain. Several vertebrae are very nicely > segmented... :P > > Just wondering if you have any suggestions for reprocessing this > subject? The error is reproducible with default recon-all settings. > > Subject has some pathology in the white matter which might be causing > the problem? > > Screenshot of T1.mgz + lh.pial at the following link: > http://imgur.com/a/uwyaq > > Thanks, > Eli Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20 hospitals, placing it for the second time on the magazine’s prestigious Honor Roll. It is also 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 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.
Re: [Freesurfer] Disastrous Soft Error
As far as I can tell, everything looks OK up until brainmask.mgz. The skullstrip step seems to have cropped out the brain and left the neck... On Fri, 2017-02-24 at 12:58 -0600, Elijah Rockers wrote: > Hello all, > > I recon-all'd ~40 different subjects. I have been going through all the > images to make sure they were processed correctly. Most required no no > editing and recon-all did a very good job. > > But for one scan in particular, it looks like Freesurfer thinks the top > of the spinal cord is the brain. Several vertebrae are very nicely > segmented... :P > > Just wondering if you have any suggestions for reprocessing this > subject? The error is reproducible with default recon-all settings. > > Subject has some pathology in the white matter which might be causing > the problem? > > Screenshot of T1.mgz + lh.pial at the following link: > http://imgur.com/a/uwyaq > > Thanks, > Eli Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20 hospitals, placing it for the second time on the magazine’s prestigious Honor Roll. It is also designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital 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 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] Disastrous Soft Error
Hello all, I recon-all'd ~40 different subjects. I have been going through all the images to make sure they were processed correctly. Most required no no editing and recon-all did a very good job. But for one scan in particular, it looks like Freesurfer thinks the top of the spinal cord is the brain. Several vertebrae are very nicely segmented... :P Just wondering if you have any suggestions for reprocessing this subject? The error is reproducible with default recon-all settings. Subject has some pathology in the white matter which might be causing the problem? Screenshot of T1.mgz + lh.pial at the following link: http://imgur.com/a/uwyaq Thanks, Eli Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20 hospitals, placing it for the second time on the magazine’s prestigious Honor Roll. It is also designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital 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 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.
