hello, I want to map a fMRI volume created with FLS onto a simplified version of the PALS surface. I tried to map it with "map to atlas" and then reduce the number of the nodes in the mesh, but that doesn't work.
Will it be OK if I choose "map to caret" and use the simplified mesh? Or do I really need to use "map tu atlas" to obtain the best fit between FSL data and the caret mesh? Thanks all AC --- Ven 9/7/10, Donna Dierker <[email protected]> ha scritto: > Da: Donna Dierker <[email protected]> > Oggetto: Re: [caret-users] caret-users Digest, Vol 82, Issue 6 > A: "Caret, SureFit, and SuMS software users" <[email protected]> > Data: Venerdì 9 luglio 2010, 21:27 > Hi Yan, > > It's tough, and I don't think I have a good solution. > You have two > problems working against you, both illustrated in the > attached capture: > > * I can't make out by eye where the cerebellum ends and the > ventral > occipital cortex begins, so Caret is also having a tough > time. This is > keeping the hindbrain from disconnecting. > > * While cranking up the WMpeak might help cause the > cerebellum to fall > off, it causes the dark white matter in motor cortex to > threshold out of > the segmentation. You have serious intensity > inhomogeneities, and I'm > not sure how well tools like FSL's fast, AFNI's > 3Duniformize, and other > bias correction utilities will be able to help you. > It looks severe. > > With the first point, it is conceivable that you could use > MRIcron, > Analyze, or something like that to zero out voxels in the > anatomical > volume at the cerebellar-occipital junction, thereby making > it easier > for the hindbrain to disconnect. (Caret isn't really > good for this > purpose, because Edit Voxels requires the volume to be > loaded as a > segmentation volume, and when you save it, the volume will > be binarized > into 0 and 255. You need to preserve the grayscale > features of the > anatomical volume to put it through segmentation, but just > zero out a > strip of voxels along several sagittal slices, to wipe out > that > cerebellar bridge.) > > But I don't know how you get around the second problem, > because it's > going to cause trouble beyond the hindbrain > disconnection. You won't be > able to find peaks that prevent fusing in brighter regions, > like the > occipital and frontal lobes, without thresholding out the > parietal lobe. > > Donna > > On 07/09/2010 01:08 PM, Ma, Yan wrote: > > Hi Donna, > > > > I uploaded both the BRIK and Head file. Their name is > CAZspgraxss1mmLPI_ACORIGIN_LH+orig. > > > > Thanks a lot, > > Yan > > ________________________________________ > > From: [email protected] > [[email protected]] > on behalf of [email protected] > [[email protected]] > > Sent: Friday, July 09, 2010 12:00 PM > > To: [email protected] > > Subject: caret-users Digest, Vol 82, Issue 6 > > > > Send caret-users mailing list submissions to > > [email protected] > > > > 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 > > [email protected] > > > > You can reach the person managing the list at > > [email protected] > > > > When replying, please edit your Subject line so it is > more specific > > than "Re: Contents of caret-users digest..." > > > > > > Today's Topics: > > > > 1. Re: Problem with Anatomical Volume > Segmentation (Donna Dierker) > > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Thu, 8 Jul 2010 16:13:54 -0700 (PDT) > > From: Donna Dierker <[email protected]> > > Subject: Re: [caret-users] Problem with Anatomical > Volume Segmentation > > To: "Caret, SureFit, and SuMS software users" > > <[email protected]> > > Message-ID: <[email protected]> > > Content-Type: text/plain; charset=us-ascii > > > > Hi Yan, > > > > Can you upload your cropped anatomical volume here: > > > > http://brainvis.wustl.edu/cgi-bin/upload.cgi > > > > I'll try to have a look at it in the morning, but I'll > be tied up all day > > beginning at 8:30am. > > > > Donna > > > > > > ----- Original Message ---- > > From: "Ma, Yan" <[email protected]> > > To: "[email protected]" > <[email protected]> > > Sent: Thu, July 8, 2010 2:43:52 PM > > Subject: [caret-users] Problem with Anatomical Volume > Segmentation > > > > Hi there, > > > > I tried several times to segment this volume with > different gray and white > > matter peak values to avoid 'Error in hind brain > segmentation'. When I finally > > went through the segmentation process, the resulting > volume is missing large > > chunk of brain. Attached is a snapshot of the > segmentation volume overlapped on > > the approximate volume appeared when setting the gray > and white matter peaks. > > Current settings are gray: 104, white: 144. > > > > Thank you, > > Yan > > > > > > ------------------------------ > > > > _______________________________________________ > > caret-users mailing list > > [email protected] > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > End of caret-users Digest, Vol 82, Issue 6 > > ****************************************** > > > > _______________________________________________ > > caret-users mailing list > > [email protected] > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > -----Segue allegato----- > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
