Covert surface images in fsaverage5 space into volume images in MNI152 space

Submitted by puyunfashi on Thu, 06/09/2022 - 09:03
  1. First covert the original image in fsaverage5 space into image in fsaverage space. If your image is in fsaverage space whatsoever, please skip this step

 

mri_surf2surf --mapmethod nnf --srcsubject fsaverage5 --trgsubject fsaverage --hemi {hemisphere: lh, rh} --sval {input_img} --tval {output_img}

 

  1. Covert the fsaverage space image into volume image, please note that now your volume image is still in fsaverage space!

 

mri_surf2vol --o {output_img} --so $FREESURFER_HOME/subjects/fsaverage/surf/lh.white {input_img} --ribbon $FREESURFER_HOME/subjects/fsaverage/mri/aseg.mgz

 

  1. Convert the volume space in fsaverage space into MNI 152 space

 

mri_vol2vol --reg $FREESURFER_HOME/average/mni152.register.dat --mov MNI152.nii.gz --targ {input_img} --inv --o {output_img}

 

where MNI152.nii.gz is the template volume, either 1mm or 2mm. eg, $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz

 

I notice that after step 3, the original values on the edge of the cluster were changed a little.

 

References:

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

https://surfer.nmr.mgh.harvard.edu/fswiki/mri_vol2vol

https://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol

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