assuming this is a surface-based analysis, then you'll need to run mri_surf2vol to convert it into a volume using fsaverage as the subject. Run it with --help to get more info

On 10/2/18 5:14 AM, Carme Uribe Codesal wrote:

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Dear FreeSurfer users,

I am trying to extract a binary mask from the file cache.th13.abs.sig.cluster.mgh (I want a ROI from the clusters p<0.05) and convert this mask into a .nii file.

I have found a previous message in the forum that reccomends using mri_binarize:

mri_binarize --i cache.th13.abs.sig.cluster.mgh --min 1.3 --o lh_AP.mgh

And from this output I have run:

mri_convert --in_type mgh --out_type nii --out_orientation RAS lh_AP.mgh lh_AP.nii

However, I can't visualize the lh_AP.mgh and of course the lh_AP.nii is not created properly when I try to visualize it with mricron.

Another command that I have tried without success is:

mri_surf2surf --sval lh_AP.mgh --tval test.nii --hemi lh

How can I get the mask to operate with it in FSL for example?

Thanks in advance!

Carme Uribe

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