[BUG] expand roi fails

[Remi-Gau]

Is there an existing issue for this?

• I have searched the existing issues

Expected Behavior

reported by @iqrashahzad14

Using a 4D beta image as data for defining space and a map from neurosynth, createRoi fails to give a ROI.

Minimal code to reproducde

opt.save.roi = true; 
opt.outputDir = pwd;

dataImage = fullfile(pwd, '4D_beta_0.nii');
zMap = fullfile('hMT.nii');

% X Y Z coordinates of right V5 in millimeters
location = [44 -67 0];

sphere.location = location;
sphere.radius = 1; % starting radius
sphere.maxNbVoxels = 200;

specification  = struct('mask1', zMap, ...
                        'mask2', sphere);

mask = createRoi('expand', specification, dataImage, opt.outputDir, opt.save.roi);

Current Behavior

No response

Error message

 Expansion:
 radius: 1.00 mm; roi size: 2 voxels
 radius: 3.00 mm; roi size: 20 voxels
 radius: 5.00 mm; roi size: 70 voxels
 radius: 7.00 mm; roi size: 192 voxels
 radius: 9.00 mm; roi size: 395 voxels
Error using maroi_pointlist (line 61)
Non integer points in voxel space - are points really of type 'real'?

Error in createRoi>saveRoi (line 296)
  roiObject = maroi_pointlist(struct('XYZ', mask.roi.XYZmm, ...

Error in createRoi (line 212)
    outputFile = saveRoi(mask, volumeDefiningImage, outputDir);

Error in MNE (line 26)
mask = createRoi('expand', specification, dataImage, opt.outputDir, opt.save.roi);

Environment

- OS: ?
- Matlab: ?
- SPM: ?

Branch

- branch: master ?
- version CPP ROI: v0.1.0

Anything else?

No response

[Remi-Gau]

@iqrashahzad14

I am looking into this with the data you gave me

1. can you make sure that the you use an actual binary mask to for hMT. You seem to be using a zMap straight from neurosynth. You must threshold it first.

See here:

CPP_ROI/demos/roi/roi_script.m

Line 161 in 7870fd6

% Threshold probability map into a binary mask

2. Also if you want to save the ROI you are creating, you must make sure that the ROI
   image you are using DOES have the same resolution as the image you will
   sample.

see here:

CPP_ROI/demos/roi/roi_script.m

Line 25 in 7870fd6

% If you want to save the ROI you are creating, you must make sure that the ROI

Take the time to go through that script.

And a word of advice: that script will work better if you do NOT rename the file you got from neurosynth. 😉

[Remi-Gau]

That being said I am going to put things in place to catch things like that in the future and maybe improve the doc.