LUNA NOTES

    Intro
    Data flow
    Analyses done
    Special notes

INTRODUCTION
    There are 33 subjects in this dataset. High resolution structural, and low resolution structural and functional scans were taken for each subject. Age range 8 to 29.

    This dataset posed a unique problem in that the high resolution structural scans (mr) were not registered to the low resolution functional scans (anti). We also received low resolution structural scans (mean) which were registered with the anti scans. The mr scans were aligned to the anti scans by registering the mean scan to the mr scan, then inverting the resulting air file to get the mr scan into anti space.

   NAMING
    This was the system used for naming.
        mr- High resolution MRI scans that are in native space. These need to be rotated into functional activation space.
        spgr- Rotated high resolution MRI scans that are in functional activation space. These are not used, however, because most of the subject's spgr images were corrupted during transfer.
        mean- Low resolution scan that is the average of all the functional scan passes over time. Gives rough idea of anatomical information so we can register the mr scan to this.
        anti- Functional activation map. This is in the same space as the mean scan. Therefore, registering the mr image to the mean will make the mr match the anti image in space. The anti maps were later separated into negative only and positive only maps (antineg, antipos, respectively).

        clean- The image has been cleaned after initial skull stripping process.
        rf- The image has been corrected for magnet inhomogeneity.

    Spaces
        mr-             native space for hi res structural scan
        fs-           functional space. Scans with this name are aligned (6 param) with the anti map.
        305orient- 305 oriented space. Scans are aligned to icbm 305 brain, 6 param no scaling.
        305-            305 space. Scans aligned to icbm 305 brain, 12 param.
        sulcal-        scans aligned to sulcal landmarks that the user has drawn

      Order of transformation
        mr   >>   fs   >>    305orient   >>   305   >>   fs   >>   sulcal
 

DATA FLOWCHART
 
 

Getting into standard dimensions  (script)		Structural image into functional space (Pipeline)		Functional space to 305orient (Pipeline)

 
 
 

ANALYSES
        Average thickness
        Average Activation
        Age vs Activation
        Age vs Thickness
        Gender vs Thickness
        Thickness Variance
        Activation Variance
        Activation vs Thickness
        (no warp versions of all above maps were done as well)