You really do need to map to atlas or directly to either/both of these files in the Caret distribution:
data_files/fmri_mapping_files/Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_FLIRT.clean.73730.coord data_files/fmri_mapping_files/Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_FLIRT.clean.73730.coord But then it seems like it should be possible to downsample to one of these simpler spheres in the distribution: ./data_files/CONSTRUCT.SPHERE/sphere.0.coord ./data_files/CONSTRUCT.SPHERE/sphere.1.coord ./data_files/CONSTRUCT.SPHERE/sphere.2.coord ./data_files/CONSTRUCT.SPHERE/sphere.3.coord ./data_files/CONSTRUCT.SPHERE/sphere.4.coord ./data_files/CONSTRUCT.SPHERE/sphere.5.coord ./data_files/CONSTRUCT.SPHERE/sphere.6.coord ./data_files/REGISTER.LVD.SPHERE/sphere.1.LVD.74.coord ./data_files/REGISTER.LVD.SPHERE/sphere.2.LVD.290.coord ./data_files/REGISTER.LVD.SPHERE/sphere.3.LVD.1154.coord ./data_files/REGISTER.LVD.SPHERE/sphere.4.LVD.4610.coord ./data_files/REGISTER.LVD.SPHERE/sphere.5.LVD.18434.coord ./data_files/REGISTER.LVD.SPHERE/sphere.6.LVD.73730.coord ./data_files/REGISTER.SPHERE/sphere.0.coord ./data_files/REGISTER.SPHERE/sphere.1.coord ./data_files/REGISTER.SPHERE/sphere.2.coord ./data_files/REGISTER.SPHERE/sphere.3.coord ./data_files/REGISTER.SPHERE/sphere.4.coord ./data_files/REGISTER.SPHERE/sphere.5.coord ./data_files/REGISTER.SPHERE/sphere.6.coord How exactly to do that, I'm not sure. John Harwell is on vacation, but perhaps David or Matt knows how. On 07/12/2010 09:31 AM, Figa Pelosa wrote: > 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 >>> >>> _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
