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!


 1) create a registration file from FSL-MNItemplate to Freesurfer space and 
        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 

 3) writing label for id = 1
        mri_cor2label --i lh.atlas.mgh --surf fsaverage lh --id 1 --l 

 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

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