Hi, I’m trying to get an atlas (Harvard/Oxford sub&cortical) into individual space via surface registration. Motivation is to replicate a finding in volume space (functional data) in a normal population with that atlas in a lesion data set where transformation to template volume space is not feasible.
I think I found a way described in principle for one region below but it seems clumsy with a lot of steps , so I’d like to check if there is a better/more accurate ways with less transforms?
Any feedback appreciated!
Thanks, Dorit
1) create a registration file from FSL-MNItemplate to Freesurfer space and fsaverage bbregister --s fsaverage --mov MNI152_T1_1mm_brain.nii.gz --init-fsl --init-header --reg mni2fsaverage.dat --T1 --o mni2fsaverage.nii
2) warp atlas from FSL-MNI space onto surface of fsaverage mri_vol2surf --mov HarvardOxford-cort-maxprob-thr25-1mm.nii.gz --reg mni2fsaverage.dat --projdist-max 0 1 .01 --interp nearest --hemi lh --out lh.atlas.mgh
3) writing label for id = 1 mri_cor2label --i lh.atlas.mgh --surf fsaverage lh --id 1 --l ./lh.1.atlas
4) move label from fsaverage onto individual subject space mri_label2label --srclabel lh.1.atlas --srcsubject fsaverage --trglabel lh.1.atlas --trgsubject subject --regmethod surface --hemi lh
5) create voluem form label mri_label2vol --label subject/label/lh.1.atlas --subject subject --hemi lh --identity --temp subject/mri/brain.mgz --o lh.1.atlas.volume.nii --proj frac 0 1 .01
6) fix wholes/border ribbon mri_binarize --dilate 1 --erode 1 --i lh.1.atlas.volume.nii --o lh.1.atlas.volumebin.nii --min 1 mris_calc -o lh.1.atlas.volumebinfixed.nii lh.1.atlas.volumebin.nii mul subject/mri/lh.ribbon.mgz
7) bring from subject T1-FS space (1mm) into subject's functional space bbregister --s subject --mov func.nii --init-fsl --init-header --reg anat2func_register.dat --bold
8) warp atlas image from individual subject anat space to subject bold space mri_label2vol --seg lh.1.atlas.volumebinfixed.nii --temp func.nii --reg anat2func_register.dat --fillthresh .5 --o lh.atlas.func.nii