I have two subjects, subA and subB. subA has a binary ROI mask, native space, that I'd like to place in subB's native space. Both subjects have been run through all stages of recon, edited, etc. Is there a better or easier way to achieve this than what I've run?:
#Resample the native space binary ROI file into "brainmask" space mri_convert -rl /subA/mri/brainmask.mgz -rt nearest --no_scale 1 ROI.nii.gz /subA/mri/ROI.mgz
#Convert ROI file into a label mri_cor2label --id 1 --c /subA/mri --i ROI.mgz --l ROI.label
#Move label from subA to subB mri_label2label --srcsubject subA --srclabel /subA/mri/ROI.label --trgsubject subB --trglabel /subB/mri/ROI_to_subB.label --regmethod volume
#Convert warped ROI label to a volume mri_label2vol --label /subB/mri/ROI_to_subB.label \ --subject subB \ --temp brainmask.mgz \ --regheader brainmask.mgz \ --o /subB/mri/ROI_to_subB.mgz
#Convert the volume back to native subB space mri_convert -rl subB_native.nii.gz -rt nearest --no_scale 1 /subB/mri/ROI_to_subB.mgz ROI_to_subB_native.nii.gz
A few follow-up questions:
1) When running mri_label2label, is better to use surface or volume for the "regmethod"? Which method will give me a better fit for my output? 2) The output I'm getting looks striped (there are holes in the binary mask) and doesn't quite fit the anatomy (the final file is shifted up and away from where I would expect it to be although in the general vicinity of what I would expect). It's almost as if I've chosen a wrong target or file along the way. I don't expect the fit to be perfect, but did I do something wrong?
Thanks in advance to any and all replies.
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