[caret-users] Sections and MRIs

[John Harwell]

On Jun 26, 2009, at 8:59 PM, Donna Dierker wrote:

>> 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.

You will need to save the cells into a cell file and then load the  
cell file as a volume cell file.

* Load your data files including the cells and the MRI volume.
* Select File Menu->Save Data File to Display the Save Data FIle Dialog.
* Set the File Type to "Cell Files (*.cell)".
* At the bottom of the dialog, set "Cells Associated With Surface" to  
the fiducial (anatomical) surface.
* Enter a File Name (volume_cells.cell) and press the Save button.
* Select File Menu->Open Data File to display the Open Data File dialog.
* Set the File Type to "Cell Files - Volume (*.cell)".
* Select the cell file that was saved in a previous step and press the  
Open button.
* Display the volume in the Main Window.
* Press the Toolbar's "D/C" button to display the Display Control.
* Set the Page Selection to "Cell Main".
* Check the box labeled "Show Volume Cells".

As long as the surface and volume are aligned, the cells should appear  
over the volume slices.  In your Q3 you mention rotating the volume.   
This could be an issue for proper display of cells over volume slices.

>> 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?

You will need a flat surface.  You will need to project the cells  
(Layers Menu->Cells->Project Fiducial Cells) with the fiducial surface  
in the main window.  Switch the display to the flat surface which now  
has cells on it as a result of cell projection.  Select Layers Menu- 
 >Cells->Convert Cell Density to Metric.  Use the Display Control to  
remove the cells and set the Surface Primary Overlay to Metric.

>>
>> 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?

We can add cebus to the list.  I don't believe any of the operations  
in Caret examine the species other than the automatic naming of new  
files.

>>
>>
>>
>> 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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-----------------------------------
John Harwell