Hi Donna, I just wanted to thank you for your reply! This was quite helpful, and I have managed to successfully clean up my images as I had hoped. It is indeed tedious, but it works.
Best Wishes, Jessica On Fri, Feb 26, 2010 at 9:59 AM, Donna Dierker <[email protected]>wrote: > Hi Jessica, > > See inline replies below. > > Donna > > On 02/25/2010 03:50 PM, Jessica Bernard wrote: > > Hello, > > > > I have been working with images of the cerebellum (and just stared > > working with CARET) that have been extracted from the whole brain, and > > I need to hand clean them to remove some of the occipital cortex to > > complete my analyses. I've searched through the archives and website > > to find the best way to do this, but I have not had much luck. Would I > > do this by hand drawing borders? > No, your problem must be addressed in the segmentation volume. It is > possible that creating a surface of the existing segmentation might help > you visualize and pinpoint "bridge" and "neck" structures that are > holding non-cerebellar tissue onto your cerebellum. Clicking on those > lets you focus on the smallest region of voxels to erase, so that then > you can do disconnect isllands, e.g.: > > File: Open Data File: Volume Anatomy file - load your T1 anatomical > File: Open Data File: Volume Segmentation file - load your cerebellum > Toolbar: D/C: Overlay/Underlay Volume: Anatomy underlay, Segmentation > overlay > Volume: Segmentation: Reconstruct into Surface > select hypersmooth surface > Switch to inflated surface -- look for cinch-like structures, where > there is a narrow bridge connecting occipital cortex to cerebellum; > click on the surface as close to the cinch as you can get > Switch to Volume and select view All > Volume: Segmentation: Edit voxels > When done, File: Save data file: Volume Segmentation File -- save as > different filename > Volume: Segmentation: Disconnect Islands > After making sure results are sane, File: Save data file: Volume > Segmentation File (overwrite) > > I must say, I do not envy your task. I don't know anyone trying to do > that. A masochistic streak might come in handy. ;-) > > Could anyone recommend a method or a useful tutorial? > Nothing specifically cerebellum oriented. General patching tips are here: > > > http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/Segmentation#Segmentation_Volume_Manual_Error_Correction > > Thank you very much, and I apologize for what might be a completely > > obvious question. > There is nothing obvious about how to segment the cerebellum accurately. > > It depends on how you are using your cerebellar segmentations, but to > get one that yielded a surface of the quality that David obtained with > the Colin cerebellum, you need cubic 0.5 voxels scanned 20 or so times, > coregistered, and averaged. Most anatomical MRI is not of that > quality. But I am guessing your analyses do not need surface > representations of the cerebellum (i.e., the segmentations need not be > that fine-grained). My reading of your needs is that you just want to > shear off occipital cortex that is hanging onto your cerebellum. > > > > Best Wishes, > > Jessica > > > > -- > > Jessica Bernard > > PhD Candidate > > Department of Psychology > > Cognition & Cognitive Neuroscience > > University of Michigan > > 4056 East Hall, 530 Church St. > > Ann Arbor, MI 48109 > > Email: [email protected] <mailto:[email protected]> > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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 > -- Jessica Bernard PhD Candidate Department of Psychology Cognition & Cognitive Neuroscience University of Michigan 4056 East Hall, 530 Church St. Ann Arbor, MI 48109 Email: [email protected]
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