[caret-users] Sections and MRIs

[Donna Dierker]

> Subject: Sections and MRIs
> From: "Peter L. Carras" <pcarras+ at pitt.edu>
> Date: Fri, 26 Jun 2009 18:43:04 -0400
> To: caret-users at brainvis.wustl.edu
>
> To: caret-users at 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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://brainvis.wustl.edu/pipermail/caret-users/attachments/20090626/8492901e/attachment.html