Hello!

I have a fsl label (from the JHU atlas) and want to overlay this on my T1 from FreeSurfer (native space) to create models in 3DSlicer. What is the best way to get these labels (one ROI with intensity 1 in a nifti) to fit the individual T1. I tried the following:

Flirt -in MNI15_T1_1mm.nii.gz -ref brainmask.nii -out converted.nii -omat convertedmatrix.mat -bins 256 -cost corratio -searchx -90 90 -searchy -90 90 -searchz -90 90 -dof 12 -interp trillinear Flirt -in JHUlabel.niig.gz -ref brainmask.nii -applyxfm -init convertedmatrix.mat -out newlabel.nii.gz

(brainmask.nii is the brainmask.mgz converted to nii using mri_convert)

Unfortunately this did not work, the label is still in the wrong position. Any idea what I am doing wrong or how I can solve this?

Thanks! Heidi