Difference between revisions of "Warping VOI masks"

Revision as of 14:18, 29 March 2010

For information on the mask type and mask creation, see Making VOI Masks.

After making a mask using the draw dataset plugin, the mask in +tlrc (Canonical VOI Masks) or +orig space (Individual VOI Masks). Both mask types are usually sampled at 1mm. In order to accurately dump timecourse data from these regions, the mask must be warped an resampled. For the sake of storage contraints and accuracy, the adwarp command should no longer be used. Adwarp typically would involve a non-optimal, additional manipulation step on the functional dataset. Instead 3dfractionize and 3dresample should be used only on the mask file to down-warp the mask to +orig and resample to match the functional dataset space (usually 3.75mm 3.75mm 4.00mm).

Canonical VOI Masks:

$ 3dfractionize -template [subject's functional dataset +orig] -input [mask file +tlrc] -warp [subject's sag116+tlrc]  -clip 0.1 -preserve -prefix [output, append 'r' to input mask name +orig]
e.g.
$ 3dfractionize -template zmidantoutreg+orig -input apVOImask+tlrc -warp sag116+tlrc -clip 0.1 -prefix apVOImaskr+orig

• Notes:

-Make sure you use subject specific files for warp and template. The template should be functional dataset you will eventually dump data from.

-Use exact coordinate spaces specified above (+tlrc/+orig)

-Clip should not be changed unless you notice that too much or not enough of the starting mask size is removed. Increase to clip additional voxels, decrease to restore.

-When the command is executed you should end with a maskfile that is resampled to the functional dataset coordinate space and down-warped to +orig space. You can verify this by using the 3dinfo command in terminal on the output mask file.

Individual VOI Masks: Custom placed VOIs based on Individual Anatomy

$ 3dresample -dxyz DX DY DZ -prefix [output, append 'r' to input mask name] -inset [input mask +orig]

e.g.

$ 3dresample -dxyz 3.75 3.75 4.00 -prefix apVOImaskr -inset apVOImask+orig