Hi Graham,

See inline replies below.

On 10/23/2006 10:05 PM, Graham Wideman wrote:
Folks:

We are trying to get up to speed on caret, and find ourselves thoroughly stalled by holes in the docs, but suspecting that we may be missing some important doc.

In particular, we really need a guide as to what everything in the UI actually does.

Case in point:

Display Control dialog: There's a great deal of functionality there, but rather inscrutable without docs: The GUI Reference Guide doesn't list the Display Control dialog, so has this not been documented, or is it documented somewhere else?
To my knowledge, the best description of the D/C dialog currently is in:

Caret 5.5 Tutorial - The Basics (including PALS atlas)
http://brainmap.wustl.edu/caret/pdf/Caret_Tutorial_Sep22.pdf

I can't find the D/C dialog in the reference manual, either.

We want to know, for example, how to operate the Metric > Threshold settings. There are Column, Average Area and User widgets -- what are they all about? We're pretty certain that they somehow filter or color the data to be displayed, but how is not clear.
I believe the column threshold stores any threshold that was input during fMRI mapping (and is stored in the metric file header). The user can override this value (without changing it) using the user column.

The Average Area column is only applicable when you are mapping group results (in volumetric form from AFNI, FSL, SPM, etc.) to the PALS_B12 atlas and you want to threshold the input volume. This is discussed a bit on pages 24 and 25 of the Basics manual (section 5.1 shows where you input the threshold), as well as page 13 of the old PALS tutorial:

PALS_ATLAS_WEBCARET_TUTORIAL_June_05.pdf
http://sumsdb.wustl.edu:8081/sums/archivelist.do?archive_id=6363282

Perhaps the best explanation of average area is in David's PALS paper, page 652, under Multi-fiducial mapping:

http://brainvis.wustl.edu/resources/-Pals.wcover.pdf

I recognize your name from the AFNI and Freesurfer lists, so I'll throw in some unsolicited tips:

* Caret thresholding isn't like AFNI's -- e.g., it won't convert t, z, or F values to p-values on-the-fly for thresholding purposes. Whatever value is in the metric file (stat, magnitudes, raw -- whatever), the threshold acts on that value.

* Unlike AFNI/SUMA, the volume/metric aren't automatically synced together. If you change the metric column, you need to manually change the functional volume column in the Overlay/Underlay - volume settings (if applicable), so that the surface activation matches the volume activation.

* There are command line scripts to streamline import of Freesurfer surfaces and generate cortical midthickness surfaces from them (http://brainmap.wustl.edu/pub/donna/SCRIPTS/FREESURFER/freesurfer2caret.sh login pub, password download).

I know you're not just a user of documentation, but also a developer of it. Thanks for helpful documents like http://www.wideman-one.com/gw/brain/fs/coords/fscoords.htm).

Thanks,

Graham
--
Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see 
http://home.att.net/~donna.hanlon for details.)

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