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Wow thanks for the quick response! -- I'll have to check on the exact calls we used -- not sure about "intref" right now. -- We are investigating your FNIRT suggestion. Beyond that, in light of the problems / issues you listed, does it seem likely that a custom model would be worth the effort -- If yes, then can we discuss getting access to the software? I think we have something like 15 hand drawn segmentations right now - the pipeline needs to process about 160 brains at several time points -- so we really want to find a valid, reliable, and automatic solution. Thanks for your help Clark -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Brian Patenaude Sent: Thursday, March 11, 2010 3:37 PM To: [log in to unmask] Subject: Re: [FSL] FIRST: Hippocampus & Older adults Hi, Are you running run_first_all? If not, are you using the "intref" model for the hippocampus? FIRST can have problems with the hippocampus in severe atrophy cases. There are some older subjects in the training set but not much with severe atrophy of the hippocampus. The problem is caused for two reasons. The shape variation is not well represented. The second is the intensity variation is not well represented in the training data. In particular, with significant atrophy the presence of CSF where either the Amygdala or Thalamus was bordering. The best solution that I've found given the models provided is to use FNIRT to warp the image into MNI space. Then run FIRST on the warped image, and transform the surface(s) back into the native space using `run_mesh_utils --doWarpMesh -i warp_field -m mesh.vtk -o out.vtk` Yes, FIRST can accommodate custom models. The software to do it has not been included in FSL. It may be possible to provide you with the software if you're interested, have to check. May I ask how many hand segmentations you have? Cheers, Brian > Dear FSL world: > > Does anyone have experience using FIRST with scans from older individuals? > We are finding that the built-in shape/appearance model for hippocampus > does not do a very good job, especially when there is significant atrophy. > The documentation indicates the existing model was generated using > &children and adults, normals and subjects with pathologies&. We are > wondering if FIRST needs a model that more closely matches our sample? We > assume that FIRST can accommodate user-generated models for specific > regions, but we have not been able to figure out how to generate something > based on hand-drawn hippocampi from a small group of older subjects. Can > anyone give us some help/advice on this issue? > > Thanks > > Clark >