External Email - Use Caution 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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