[caret-users] Visualizing functional data normalized to SUIT

[Donna Dierker]

Hi Janine,

Your message was addressed to caret-users-owner at brainvis.wustl.edu, 
which is aliased to me.  But in order for it to go to all of the 
caret-users mailing list, the address should be 
caret-users at brainvis.wustl.edu, which I have cc'd.  If you are not a 
member of caret-users, then you probably won't see replies from other 
users (e.g., Joern Diedrichsen, John Harwell or David Van Essen), unless 
they explicitly paste your address in the To or CC fields, rather than 
simply replying all.

Anyway, I have a few inline replies of my own below.

Donna

On 04/21/2008 04:40 AM, J D Bijsterbosch wrote:
> Dear CARET users,
>
> I would like to visualize functional MRI group results to a flattened
> cerebellar
> atlas. I have normalized my images using the SUIT cerebellar template and would
> like to visualize this using CARET. The SUIT package provides a spec file and I
> have attempted to visualize my results using 'map volume(s) to surface(s)' in
> CARET. However, my results are not the same as they are in SPM5.
>   
I had to google it, but I see this is Joern Diedrichsen's contribution:

http://www.bangor.ac.uk/~pss412/imaging/suit.htm

Looks pretty cool!  I knew about the Caret toolbox, but much of this is 
news to me.

This section looks expecially relevant:


    Spatial unbiasedness, and the relationship to MNI space

I think there's a pretty good chance Joern's still on the mailing list, 
so I hope he might help.
> I am unclear about the steps to be taken and the meaning of for example the
> thresholding and color-coding in the final image. The tutorials and quick
> guides are not very helpful as they only tell you what to click for the
> standard case with provided data and do not explain the meaning of each step.
>   
Thresholding in Caret is straightforward -- perhaps too straightforward 
at times.  For example:  Say you are trying to visualize a map of 
t-stats overlaid on your anatomical volume.  Then entering "+3.0" for 
the positive threshold in the metric settings page will make any voxels 
with t-stats less than 3.0 display with no overlay.  Only voxels whose 
t-stats exceed 3.0 will have overlay coloring.  Caret does not convert 
stat volumes to p-values, so if you don't see activation where you 
expect it to be, then look for these common causes:

* The origin or orientation of your functional volume doesn't match the 
surface/anatomical.
* You're trying to map a NIfTI .hdr/.img pair, which Caret doesn't yet 
support.  Convert it to .nii.
* The palette is scaled such that your values are in the zero bin.

If you toggle on Display Color Bar on the metric settings page, the min 
and max of the color scale will be shown, along with the whole color 
spectrum.  There are several built-in palettes available, or you can 
make your own palette 
(http://brainmap.wustl.edu/caret/caret_help/file_formats/file_formats.html#paletteFile).  
The Attributes: Palette: Edit menu gives you a graphical user interface 
for this purpose.

Have you had a look at this tutorial:

http://brainmap.wustl.edu/caret/pdf/Caret_5.5_UserGuide_Analysis.pdf

It is less heavy on the scenes and more nuts and bolts oriented, I find.
> I hope someone can help clarify the steps in CARET so that I can visualize my
> results successfully.
>   
If no one else has more specific suggestions within the next few days, 
and the tutorial above doesn't address your questions, then feel free to 
upload one of your group results volumes that you wish to map.  I'll 
give it a shot and let you know how I fare.
>
> Best wishes,
>
>
> Janine Bijsterbosch
>
>
> Academic Clinical Psychiatry
> University of Sheffield
> United Kingdom
>