If I correctly understood your question, you have registered your native space to the MNI-space. After this step, you imported the Brainnetome ROIs to your native space using the inverse warp (or inverse matrix).

If this is correct, you would need to compute the total gray and white matter volume in the full brain. So, in my opinion, the idea would be to compute the tissue-class segmentation. You can use FAST program, included in FSL which is an implementation of the hidden Markov random field algorithm (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FAST). There are many other options such as atropos, included in ANTs (Article An Open Source Multivariate Framework for n-Tissue Segmentat...

Once done, you can intersect your native space ROIs with the GM segmentation. Being NULL all those voxels not equal to '1' in the GM map (just mask the ROI map according to GM segmentation).

I hope this helps.

Joan.

If you use, FreeSurfer or FSL, it would automatically, provide each vols of interest. else, you could make a mask and get the vols.

Do refer to the website for detailed info.

https://surfer.nmr.mgh.harvard.edu/fswiki/Tutorials

Cheers

I agree with @Samson Nivins, FreeSurfer might be a good option. However, I would say this atlas (Brainnetome) is not implemented on Freesurfer's pipeline ('recon-all'). So you will need to use just the 'aseg.mgz' (or just the cortical ribbon maybe?) segmentation to intersect with your Braintomme ROI map. So, I'm not sure if it's worthy to implement a cortical-based reconstruction just to use one of the voxel-based outputs (especially considering that Freesurfer is computationally demanding). Perhaps you can apply just the first steps of Freesurfer's pipeline...

Hi Muhammad,

regardless of the method of ROI creation, one of the easiest ways to process ROIs/Nifti files in bulk are the FSL command line tools. For ROI volume fslstats would be the tool of choice, a bit a of bash scripting for iterating over your ROI files and you're done.

For GM-only volumina you could project a grey matter tissue MNI template into subject space and use e.g. fslmaths to compute an intersection with your ROIs.

Best,

Martin