Hi - in order to work with hi res monkey data (250um) I manually removed the cerebellum and hindbrain. there was no skull etc.
similarly for freesurfer. surefit might take some time. It did work with manual removal and a lot of time manually editing voxels. downsampling to 1mm and running recon-all then refining the surfaces with 500um in freesufer may be the best approach if the 500um data fits into 256 cubic voxels. since I believe the HCP uses 700um T1 there may clues in that literature. mris_refine in freesurfer is the command I think best Colin On 14 October 2014 18:00, <caret-users-requ...@brainvis.wustl.edu> wrote: > Send caret-users mailing list submissions to > caret-users@brainvis.wustl.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://brainvis.wustl.edu/mailman/listinfo/caret-users > or, via email, send a message with subject or body 'help' to > caret-users-requ...@brainvis.wustl.edu > > You can reach the person managing the list at > caret-users-ow...@brainvis.wustl.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of caret-users digest..." > > Today's Topics: > > 1. Hi res recon (Dr. Aditya Tri Hernowo, Ph.D) > 2. Re: Hi res recon (Donna Dierker) > > > ---------- Forwarded message ---------- > From: "Dr. Aditya Tri Hernowo, Ph.D" <adityatrihern...@gmail.com> > To: <caret-users@brainvis.wustl.edu> > Cc: > Date: Tue, 14 Oct 2014 17:25:37 +0700 > Subject: [caret-users] Hi res recon > Dear users & experts, > > Does anyone have any experience with reconstructing the cortex on 0.5mm > resolution T1 images? I am still having problems with the very long time it > takes to perform automatic error correction (more than 3 hours before the > software finally crashed). > > Regards, > > Aditya Hernowo > > > > > ---------- Forwarded message ---------- > From: Donna Dierker <do...@brainvis.wustl.edu> > To: "Caret, SureFit, and SuMS software users" < > caret-users@brainvis.wustl.edu> > Cc: > Date: Tue, 14 Oct 2014 10:38:11 -0500 > Subject: Re: [caret-users] Hi res recon > Hi Aditya, > > On monkeys, yes. Humans, no. The SureFit algorithm that is in Caret's > segmentation feature was designed for cubic 1mm human data. It worked > reasonably well on higher res monkey data, but some of the subroutines will > likely break on higher res human data (e.g., disconnecting eye, skull, > hindbrain). > > I'd turn all error correction features off and sanity check the initial > segmentation. If the skull, eye, or hindbrain is still connected, then > resolving that issue should precede the error correction steps. > Unfortunately, that will likely take some work. > > Donna > > > On Oct 14, 2014, at 5:25 AM, "Dr. Aditya Tri Hernowo, Ph.D" < > adityatrihern...@gmail.com> wrote: > > > Dear users & experts, > > > > Does anyone have any experience with reconstructing the cortex on 0.5mm > resolution T1 images? I am still having problems with the very long time it > takes to perform automatic error correction (more than 3 hours before the > software finally crashed). > > > > Regards, > > > > Aditya Hernowo > > > > _______________________________________________ > > caret-users mailing list > > caret-users@brainvis.wustl.edu > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > >
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