[caret-users] question

[Donna Dierker]

Hi Joost,

The Fornito paper used a ROI approach, i.e., the cingulate sulcus.  It 
looks like they took great pains to define the region consistently 
across subjects, as is the norm; ROI definition (and consistent 
delineation) is often the hard part.  Assuming Freesurfer 4.05 is new 
enough to have the cortical parcellation, perhaps you can use it to 
define your cingulate sulcus.

In caret-land, you can then approach things two ways:

* Without registration:  Skip registration.  Somehow export a 
parcellation from Freesurfer that, for each node, assigns 0 to nodes 
outside the ROI, 1 to nodes inside it.  Then, use caret_command 
-surface-roi-statistical-report and each subject's surface_shape file to 
output the mean depth in the ROI.

* With registration:  Register your subjects to the PALS atlas.  Somehow 
represent the ROI in the PALS standard mesh (perhaps by creating a 
probabilistic atlas of registered Freesurfer parcellations and then 
thresholding it).  Then, use caret_command 
-surface-roi-statistical-report and each subject's surface_shape file to 
output the mean depth in the ROI.  The advantage of this route is that 
you can do more than just output a summary stat for an entire region, 
which may not be very informative.  You can instead create a t-map (or 
f-map) across groups/hemispheres, which gives you greater spatial 
specificity (e.g., see tmap figure in  
http://dx.doi.org/10.1016/j.neuroimage.2008.07.034).  The latter can be 
done on either an entire hemisphere or restricted to a ROI (the latter 
being represented by a custom CUT topo file that excludes nodes outside 
the region).

While registration gives you more analytic options, it also is work.  We 
have an automated border drawing script, but it's not ready for public 
consumption yet.  For now, you still need to register as defined here:

http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html/
http://brainmap.wustl.edu/caret/pdf/Caret_5.5_Tutorial_Segment.pdf

Attached is a list of potentially useful caret_command features.

Donna

On 09/05/2008 08:35 AM, j janssen wrote:
> Hi,
>
> i´m using Caret5.6.
>
> i´ve used Freesurfer (4.05) to create white and pial surfaces.
> my goal is to use these surfaces to get measures of sulcal depth for a 
> brain region (either a hemisphere or a specific sulcus), so that these 
> can be statistically compared, such as in Fornito et al 2008, HBM 29: 
> 478-489. after various steps i´ve succesfully used "caret_command 
> -surface-identify-sulci" on the brains in my dataset. does anybody 
> have some pointers as how to proceed from this point?
>
> thanks a lot,
> -joost
>
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