Thanks for the recommendation. That makes sense! De : Glasser, Matthew [mailto:[email protected]] Envoyé : 28 novembre 2016 13:48 À : Harms, Michael <[email protected]>; Jean-Francois Cabana <[email protected]>; '[email protected]' <[email protected]> Objet : Re: [HCP-Users] Correct surface reconstruction defect
Also I would recommend using fat saturation on the T1w image in the future to avoid this kind of error. Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of "Harms, Michael" <[email protected]<mailto:[email protected]>> Date: Monday, November 28, 2016 at 9:59 AM To: Jean-Francois Cabana <[email protected]<mailto:[email protected]>>, "'[email protected]<mailto:'[email protected]>'" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Correct surface reconstruction defect Hi, In the context of FS, that is a pretty simple edit to the brainmask.mgz. Unfortunately, the HCP Pipelines don't easily support the common FS edits at this time. It is on our "to-do" list however. cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: [email protected]<mailto:[email protected]> From: <[email protected]<mailto:[email protected]>> on behalf of Jean-Francois Cabana <[email protected]<mailto:[email protected]>> Date: Monday, November 28, 2016 at 9:51 AM To: "'[email protected]<mailto:'[email protected]>'" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] Correct surface reconstruction defect Dear HCP community, I have a problem with FreeSurfer surface reconstruction for one of my subjects. Surface reconstruction is ok for the most part, but some parts in the upper brain are bad. The surface extends outside the brain and into the skull, and misses parts of the GM. How could I fix this? I guess I should stop the FreeSurferPipeline.sh at some point and correct FS intermediate output before continuing. I'm just not sure where I should break the processing and what I should do at this point? Here is an example of one of the defect I have to correct : [cid:[email protected]] Cheers, JF _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
