maroi_image ERROR (line 34) params.vol = spm_vol(params);

[ilaria sani]

Dear All,

I am trying to batch script roi extraction from image (nii) to then perform ROI analysis over multiple ROIs and subjects.

I am using the example lines provided:
fname = roi_list{1};
roi = maroi_image(fname);

I get an error early on while loading the roi.

I have seen a couple of posts that resolved a similar issue by adding marsbar('on'). It didn't work for me.

I tried to versions of matlab: 2016b and 2019a - same error

I am using spm8

I am able to use the line params.vol = spm_vol(params) outside the script.
So it must be something (trivial) related to how params is defined, but I am unable to spot it.

Can anyone help please?

Thanks,
Ilaria

[ilaria sani]

I thought I had found a workaround by using

fname = spm_vol(roi_list{i1}); % instead of fname = 'image.nii'
roi = maroi_image(fname);
roi = maroi_matrix(roi);

the script now runs without errors and roi.mat is generated.

However, when I attempt to visualize the rois from marsbar - roi definition - view
They do not appear in the gui in the folder where they are. Thus I understand that marsbar does not recognize them.

Does anyone have a clue?

I noticed that the there is one difference between the roi build via scripting and via gui:
the label field is empty:

val =

[maroi_matrix - 11 - binarized]

    label: ''
   source: 'C:\00_WAF_lab\2018_humanDTI\0_revision\2020_roi_analysis\sub-HS40\dt-neuro-rois_merged\rois\11_roi.mat'
 binarize: 1
roithresh: 0.5000
 spm_hold: 1


  dat: [158×190×136 double]
  mat: [4×4 double]
maroi: [1×1 maroi]

Can this be the problem?

Thanks!
Ilaria

[Matthew Brett]

I'm really sorry I missed this one. If you still haven't solved this - can you post over at https://marsbar.discourse.group/ ?