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[wiki:Self:FsTutorial top] | [wiki:Self:FsTutorial/FuncOverlay previous]

== Visualizing the parametric map overlayed onto structural data ==

To load the parametric map of brain activation as an overlay onto the FreeSurfer anatomical data, run these commands:
{{{
cd $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs
setenv SUBJECTS_DIR ${PWD}
qmedit -o ./spm001.img -r ./register.dat
}}}
Qmedit is simply a front-end for [wiki:Self:FsTutorial/Tools tkmedit], with some extra specifications for displaying overlays. In this command line, the {{{-o}}} option indicates the overlay, and the {{{-r}}} option specifies a registration matrix (usually use the same matrix that aligns the functional volumes with the anatomical reference). [wiki:Self:FsTutorial/Tools Tkmedit] should start and display something like the following:

attachment:qmedit-up.jpg
attachment:qmedit-down.jpg

Coronal, saggital and horizontal (axial) views can be displayed in the image window by clicking the labeled buttons on the GUI, and different slices in the volume are selected changing the value of Slice. Zooming in and out on the image window are accomplished with either clicking the labeled buttons or changing the numerical value.

As mentioned previously, the overlay's colormap is by convention and default a "heat" scale, with blue to cyan indicating increasingly negative values, and red to yellow indicating higher positive values. The overlay can be turned off by checking the '''View->Functional Overlay''' option.

To modify other aspects of the colormap, explore the options in '''View->Configure->Functional Overlay''':
 * '''Reverse values''' will display negative values in warmer colors, and positive values in cool ones;
 * '''Grayscale''' will use a greyscale color scale instead of the normal blue to red heat scale. The most negative values will be shown in black and the most positive values in white;
 * '''Opaque''' will cause the overlay to be completely opaque;
 * '''Threshold minimum / midpoint / slope''' configures the colormap. {{{Min}}} specifies the threshold below which values will be transparent, or not visually represented on the overlay. {{{mid}}} defaults to orange, {{{max}}} defaults to yellow, and all values above this are drawn in yellow as well. {{{max}}} is determined by the {{{slope}}} value according to: {{{max = (1.0/slope) + mid }}} [[BR]]
In all cases,the Apply button must be clicked in order for the changes to take effect.

The '''View->Mask to Functional Overlay''' option effectively masks the anatomical volume with the opaque regions in the overlay volume. Using this option and turning off the overlay may yield a better sense of which anatomical regions were active during the study. (this option may not currently work well.)