[caret-users] importing MD Plot files into caret

[John Harwell]

Hi Michelle,

Do you know what units your contours are in?  Caret assumes the  
contours are in millimeters and if your contours are in a smaller  
scale, say micrometers, they will need to be rescaled so that they  
can be seen.

Contours can be rescaled by:

* Load the contours so that the model in the Main Window is Contours.
* Select Window Menu->Transformation Matrix Editor.
* Near the bottom of the Transformation Matrix Editor Window, press  
the Scale button and enter the desired scale factor (if your contours  
are in micrometers, enter 0.001 to convert them to millimeters).
* Press the Apply Matrix to Main Window button and a small window  
will pop up.  Check the boxes next to Main Window Contours and Main  
Window Contour Cells, and press the OK button.
* Press the Close button on the Transformation Matrix Editor Window.
* Press the "R" button in the Main Window Toolbar.  You should see  
your contours.

If the problem with the contours is not a scaling issue, contact me  
so that I can get your MDPlot file and determine the problem.

-----------------------------------
John Harwell
john at brainmap.wustl.edu

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave   Box 8108
Saint Louis, MO 63110


>
> Subject:
> importing MD Plot files into caret
> From:
> Michelle Morrow <mim37+ at pitt.edu>
> Date:
> Thu, 01 Nov 2007 16:44:06 -0400
>
> To:
> "Caret, SureFit, and SuMS software users" <caret- 
> users at brainvis.wustl.edu>
>
>
> I would like to display histological data (labeled neurons in a  
> macaque brain) using Caret.  To do this, I would like to import MD  
> Plot files of my sections.
> I first open the caret program, then choose "import file" from the  
> file menu, then select a single file to open.  According to the  
> "contours and sections" tutorial, cells should be imported as  
> contour cells, and lines should be imported as contours, and away I  
> go.  However, I see nothing after I import.
>
> Am I missing a step?
> Thank you - Michelle
>
> Michelle Morrow
> University of Pittsburgh
> mim37 at pitt.edu
>
>
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