I'm looking forward to get some help from them.. AC --- Lun 12/7/10, Donna Dierker <[email protected]> ha scritto:
> Da: Donna Dierker <[email protected]> > Oggetto: Re: [caret-users] simplified mesh and metric files > A: "Caret, SureFit, and SuMS software users" <[email protected]> > Data: Lunedì 12 luglio 2010, 15:15 > 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 > _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
