Osprey Voxel Overlap Heatmap Problem

MRS Software Osprey
1

Dear experts,

I’m trying to run osp_plotVoxelOverlap on my data. I’m running MEGA-PRESS data through the standard Osprey pipeline in a release downloaded Monday, Feb 13, 2023.

Currently the output looks like this:

GABApaper_voxeloverlapfigure
GABApaper_voxeloverlapfigure1700×800 94.5 KB

The heatmap looks OK, but two of the three views are on the wrong slice. It looks to me like the center of mass of the voxel mask may not be setting up correctly in osp_extract_three_plane_image_overlay. Is there an easy fix for this?

I’m happy to provide any other information needed!

Thanks!

2

Hi @markb,

Osprey is trying to determine the voxel center automatically as the center of mass of all masks, but obviously fails in your case.

A trick to overwrite this is to add a second input to the osp_plotVoxelOverlap function like this:

out = osp_plotVoxelOverlap(MRSCont,[1 -51 43])

with the second argument being the center coordinates. You can quite easily find the correct ones by opening the heat map first Osprey’s nii viewer with the full path to the heatmap:

nii_viewer({'/fullpath/derivatives/VoxelMasks/PRESS_35_act_space-scanner_mask_VoxelOverlap.nii.gz'}))

Next you find the slices you want and the three small numbers in the top right corner (see image) are the coordinates to parse as the second argument.

image
image1394×1626 120 KB

Best,
Helge

3

Hi @Helge ,

Thank you! This works perfectly.

Warmly,

Mark