> Subject: Sections and MRIs > From: "Peter L. Carras" <pcarr...@pitt.edu> > Date: Fri, 26 Jun 2009 18:43:04 -0400 > To: caret-users@brainvis.wustl.edu > > To: caret-users@brainvis.wustl.edu > > > Hello, > > I recently started using CARET (v5.61). I have had some success, but > also a few questions that do not seem to be covered in the tutorials. > We have macaque brains with both MRI images and histological > sections. The layer four contours for the sections of a left frontal > cortex were traced in MDPlot. I have successfully imported the > contours into CARET, along with the labeled neurons found in each > section, and saved them as a spec file. I also opened the MRI image > of the whole head in CARET, segmented it, and saved the left cortical > surface as another spec file. > > Q 1 - Is it possible to display the labeled neurons from the section > data on the MRI image of the complete cortex? If so, how would I go > about doing this? The histological sections were cut in the coronal > plane, and extend caudally only to the posterior commissure. > Q 2 - When the contours were originally drawn, successive sections > were aligned on the dorsal-medial boundary of each section. The > cortical fiducial surface as reconstructed by CARET is therefore > somewhat distorted - the sulci are visible but the dorsal edge of the > medial wall is flat rather than curved. Will this cause the labeled > neurons to appear in incorrect locations when they are displayed on > the MRI-based surface? If so, can you suggest a way to correct the > surface (short of re-tracing all 390 sections)? > > Q 3 - The SureFit segmentation algorithms were unable to successfully > operate on the MRI image, even when I tried varying the default gray > matter and white matter peak values. Typically, the program stopped > and reported an error in the eye fat segmentation step, or an error in > hindbrain segmentation. When I de-selected those steps, CARET crashed > when determining layer 4 or filling the ventricles. I ended up > segmenting most of the brain manually. Do you have advice on how to > increase the likelihood that SureFit will succeed in segmenting a > macaque MRI image? The MPRAGE scan was done on a 3T Siemens Allegra > scanner with 0.7 mm isotropic voxels, and was rotated in CARET to LPI > orientation. > > Q 4 - Is it possible within CARET to convert the map of labeled > neurons (shown as contour cells on the fiducial surface) to a map of > cell density? > > Q 5 - In addition to the data on macaques, we also have anatomical and > MRI data from new world monkeys (Cebus apella). Do you anticipate > adding Cebus to the list of species in the Metadata category? > > > > Your advice or assistance would be much appreciated. > > Sincerely, > Peter Carras >
-- Peter L. Carras, Ph.D. Systems Neuroscience Institute University of Pittsburgh
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Hello, Earlier today I subscribed to the CARET users mailing list, caret-users@brainvis.wustl.eduand received a "Welcome to the 'caret-users' mailing list" message. About a half hour later I posted a query to the list, but it was automatically rejected. The rejection message suggested that I contact you. Perhaps I posted to the list too soon after registering? Or perhaps the automated mail system was confused by my email address, as our university's outgoing mail program currently adds a + character to the username (changing pcar...@pitt.edu to pcarr...@pitt.edu). My original query is appended below. Could you send it to the list for me? Thanks, Peter Carras caret-users-ow...@brainvis.wustl.edu wrote: You are not allowed to post to this mailing list, and your message has been automatically rejected. If you think that your messages are being rejected in error, contact the mailing list owner at caret-users-ow...@brainvis.wustl.edu. -- Peter L. Carras, Ph.D. Systems Neuroscience Institute University of Pittsburgh |
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