[caret-users] newbie question

John Harwell john at brainvis.wustl.edu
Thu Jun 14 09:47:52 CDT 2007


Sasha,

Normally, sulcal depth measurements are generated as part of Caret’s  
SureFit segmentation algorithm.  A “cerebral hull” volume is created  
by applying 6 iterations of dilation followed by 6 iterations of  
erosion (essentially a “closing” operation).  This fills in the  
sulci.  After the dilation and erosion, the volume is logically  
“or’ed” with the segmentation volume to create the final cerebral  
hull volume.

Producing sulcal depth will require some use of the “caret_command”  
program that performs operations on the command line.
1)    Use caret_command –volume-create to create a volume.  Running  
“caret_command –volume-create” will provide information about how to  
create a volume file.  The volume will need to be in the same  
stereotaxic space as your surface.  Make the output file name  
“segmentation.nii”.  You could run “caret_command  -volume-info   
<your-anatomical-volume-file-name> to get information about inputs  
for creating a volume.
2)    caret_command –surface-to-segmentation-volume  <fiducial-coord- 
file-name>  <closed-topo-file-name>  segmentation.nii
3)    Start Caret and load your fiducial coordinate file and the  
closed topology file.  Select File Menu->Open Data File.  Set the  
File Type to Volume Segmentation Files.  Choose segmentation.nii.   
Press the Open Button.  Use the model selection control to switch  
from FIDUCIAL to VOLUME.  You should see a red segmentation volume in  
the main window.
4)    Select Volume Menu->Segmentation->Generate Cerebral Hull  
Volume.  This process should create both the CerebralHull volume and  
the VTK file, CerebralHull.vtk.  The files are automatically saved.
5)    Select Surface Menu->Measurements->Generate Sulcal Depth.  The  
fiducial surface should be listed at the top.  If the vtk file name  
is not listed, press the VTK Select button and choose the VTK file.   
Press the OK button.  This command may take a while to run.
6)    Select File Menu->Save Data File.  Set the File Type to Surface  
Shape, enter a name for the file and press the Save button to save  
the surface shape file that now contains depth information.
7)    Press the D/C button in the main window toolbar.  Set the  
Underlay to Shape and change the selected column to Depth.  You  
should now see the depth measurements on the surface.

Good Luck.

----------------------------------------------------------
John Harwell
john at brainvis.wustl.edu
314-362-3467

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

On Jun 13, 2007, at 5:55 PM, Sasha Wolosin wrote:

> Dear Caret users,
>
> I am interested in using Caret to get sulcal depth values from  
> FreeSurfer files.
>
> Following instructions on page 13 of the "User's Guide to Analysis  
> Procedures", I was able to import a FreeSurfer file  
> ("lh.smoothwm.asc") as  .spec, .topo, and .coord files in Caret5.5,  
> and also view the surface.
>
> When I attempted to generate a sulcal depth file, a ".vtk" file was  
> requested.  What is a .vtk file and how do I create one?
>
> Also if anyone could please point me to more documentation on  
> generating sulcal depth or .vtk files, I would greatly appreciate it.
>
> Thanks,
> Sasha
>
>
> Sasha Wolosin
> Research Assistant
> Developmental Cognitive Neurology
> Kennedy Krieger Institute
> 707 N. Broadway
> Baltimore, MD 21205
> ph: (443) 923-9270
> wolosin at kennedykrieger.org
>
>
>
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