====== NeuroElf (NE) - BrainVoyager (BV) ======

===== Cluster threshold =====

Both in BV and NE: VTC (functional) voxel is used, for example, for monkey data with VTC resampled at 1 mm, 1 “voxel” = 8 * 0.5 (anatomical MRI) voxels.

E.g., 10 voxels: 80 0.5 voxels, thus cluster threshold “10 voxels” means at least 80 0.5 voxels, 10 mm^3.


**Important difference:**
In BrainVoyager, when using "Interpolate" option, the number of voxels is apparently calculated after interpolation, but in NeuroElf, the threshold (k-thresh) is first applied and then the resulting clusters are interpolated. This can result in discrepancy between BV and NE, with less activated clusters in BV as compared to NE.

===== VOIs =====

VOIs that were created in NE look like mosaics when displayed in BrainVoyager. The function //ne voi_addvoxels.m// (see Dropbox\DAG\Sources\bv_umg\_4NeuroElf) adds the missing voxels. When input shift_vois is set to 'noshift' (default) the resulting VOIs will fully overlap with the VMP voxels they were derived from. When setting shift_vois to 'shift' the resulting VOIs will be shifted by 1 voxel in order to capture the actual VTC voxels they belong to. This may be important because NE can only extract time courses from original VTC voxels.

Background: There is an issue with BrainVoyager VTC voxel time courses and different time course extraction methods in NE (vtc.VOITimeCourse vs. vtc.VOITimeCourseOrig).

**Important:** If you want to look at the VOIs with a corresponding VMP, you must disable interpolation in the Volume Maps tab in BrainVoyager.