On 10/24/2006 01:58 PM, Graham Wideman wrote:
Donna:

Thanks for your quick reply (and yes, apparently we've crossed paths on those "other lists" :-). You have indeed alerted us to some places in the docs that we missed before. And your additional comments were helpful too.

But needless to say, more questions/comments:

1. Average Area: As I now understand it, this applied to the MFM procedure, and is the total area above threshold, calculated by sampling the voxel data (eg: fMRI activation) using each of the 12 B12 surfaces in turn, and then averaging those 12 totals together. Main use: adjusting thresholds for the MFM procedure to give results comparable to the AFM procedure. Right?
Comparable, but different in a couple of important respects. The AFM will give you values that haven't been "messed with" -- i.e., if using enclosing voxel mapping method, then each node in the PALS_B12 average fiducial (whichever space you selected -- AFNI, flirt, SPM2, 711-2C) will be assigned the intensity value of the voxel enclosing it. No averaging happens at the volume level. The averaging happens at the surface coordinate level and has been packaged in your caret release (in caret/data_files/fmri_mapping_files).

MFM is comparable in the sense that both AFM and MFM are for mapping group results onto a multi-subject surface atlas, but MFM intersects each of the 12 PALS subjects surfaces with the volume, and then averages in surface-land. (And if you threshold the volume going into the mapper, then it will compute the suprathreshold surface area for each subject, to generate an average suprathreshold activation area, and set the average area threshold such that this much area is supra-threshold.) So your data values get massaged -- clearly not what you want for ROI type volumes, and often not what you want for your stats. But it may better represent the potential extent of your blob and the uncertainties with this method.

2. Mid-cortex surfaces, and your FS-related suggestion: Where we use your provided surfaces to sample (map) the fMRI data, we think we should be using mid-cortical or pial surfaces, but the surfaces that the tutorial leads us to appear to be grey/white boundary surfaces. Are we thinking straight on this, and are there mid-cortical versions of PALS-B12 in AFNI+tlrc space, for example?
All the PALS_B12 surfaces are mid-cortical thickness surfaces. (In fact, Caret doesn't generate GM/WM and pial surfaces; it only generates a midthickness aka "fiducial" surface.) If you average your Freesurfer pial and white surfaces, they'll look remarkably similar to Caret fiducial surfaces. You won't see razor sharp gyri on our surfaces.

Yes, there are PALS_B12 surfaces in AFNI+tlrc space. Note that the registration was done before @auto_tlrc, using the marker method in AFNI. Details on the space flavors and how they got that way are here:

http://brainvis.wustl.edu/help/pals_volume_normalization/
3. "volume-averaged group data": This phrase shows up in a few places, and we're puzzling over whether it means something different or special compared to what we *think* it means. Eg: on p67 of Caret_Tutorial_Sep22.pdf:

"Many fMRI studies are analyzed by registering the MRI volumes from individual subjects to a standard stereotaxic atlas, then carrying out statistical analyses on the volume-averaged group data."

I think the phrase "carry out statistical analysis on volume-averaged group data" possibly refers to "voxelwise statistics, using subject variables for grouping"? Eg: 256x256x256 voxels by 10 subjects go in, 256x256x256 voxels-worth of means, t, z or whatever come out.
This is what we mean. "Voxelwise statistical output maps for group studies" is probably a better term than "volume-averaged group data." You've done your intersubject analysis in volume-land and you want to visualize it on a surface, but aren't sufficiently motivated to reconstruct your individual subjects' surfaces; then map it to PALS_B12.

Or is there something more to it? If it's a different concept, what is the "group data" that is being averaged over a volume, and then what is the statistical analysis that is performed upon it?
No -- this is it.

Thanks,

Graham

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

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