Hi,
 
I want to turn a fsaverage-label (lh.DLPFC.label) into a mask (nifti) in MNI space and used these two commands:

1) To turn the label into a volume (within $SUBJECTS_DIR):

mri_label2vol --label lh.DLPFC.label --subject fsaverage --temp ./fsaverage/mri/brainmask.mgz --o left_DLPFC_july19b.nii.gz --identity


2) To turn the DLPFC nifti into MNI space:

 mri_vol2vol --mov left_DLPFC_july19b.nii.gz --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --o left_DLPFC_MNI_july19b.nii.gz --interp nearest --reg $FREESURFER_HOME/average/mni152.register.dat


However, even though the final output file is in MNI, the ROI doesn't align with the MNI152 brain. Could it be that the FSL and the FS MNI152 brain are not the same and therefore the registration file is not the right one to use? 

Thanks for your help,

Esther

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