Extracting volume info from structural MRIs

[cgohil8]

In osl:

• We use this function to extract the dimensions from a nifti file: osl.source_recon.rhino.utils._get_vol_info_from_nii.
• Note, mri_depth=dims[2] in this function.
• This is used in the forward modelling to setup the source space grid in the function osl.source_recon.rhino.forward_model.setup_volume_source_space.
• The vol_info is passed to the MNE function mne.source_space._make_volume_source_space here: https://github.com/OHBA-analysis/osl/blob/main/osl/source_recon/rhino/forward_model.py#L375.

Links:

• osl.source_recon.rhino.utils._get_vol_info_from_nii: https://github.com/OHBA-analysis/osl/blob/main/osl/source_recon/rhino/utils.py#L154.
• osl.source_recon.rhino.forward_model.setup_volume_source_space: https://github.com/OHBA-analysis/osl/blob/main/osl/source_recon/rhino/forward_model.py#L228.

In MNE:

• There is an equivalent function for setting up the source space grid: mne.source_space.setup_volume_source_space.
• It too calls mne.source_space._make_volume_source_space here: https://github.com/mne-tools/mne-python/blob/main/mne/source_space.py#L1746.
• However, the vol_info passed to _make_volume_source_space is created here using mne._freesurfer._get_mri_info_data.
• Note, mri_depth=dims[1].

Links:

• mne.source_space.setup_volume_source_space: https://github.com/mne-tools/mne-python/blob/main/mne/source_space.py#L1504.
• mne._freesurfer._get_mri_info_data: https://github.com/mne-tools/mne-python/blob/main/mne/_freesurfer.py#L125.

So the question is what should be used for the vol_info passed to mne.source_space._make_volume_source_space?

Note:

• For MNE, they specify the mri argument passed to mne._freesurfer._get_mri_info_data , should be a mgh or mgz file in their documentation: https://github.com/mne-tools/mne-python/blob/main/mne/source_space.py#L1528-L1535.
• An mgh/mgz file is created using freesurfer
• According to https://cran.r-project.org/web/packages/freesurferformats/vignettes/freesurferformats.html#:~:text=A%20conformed%20FreeSurfer%20volume%20like,single%20time%20point%20or%20frame, freesurfer will produce volume dims of 256x256x256.

An example of a nifti file where the volume dimensions do not have mri_depth=mri_height is any of the structurals in the Wakeman-Henson dataset.