Dear FreeSurfer community,

I am trying to obtain subcortical segmentation masks for a group of healthy

volunteers using FreeSurfer v5.1 running on Ubuntu 12.10. I need the masks

to be in the native space of the original 1mm^3-isotropic 256*256*160

T1-weighted images. I found a helpful link which seems to answer my need:

http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat

Running it seems to produce good results when overlaid on top of the original

images. However, I couldn't find any mention in either the newsgroups or the

wiki as to whether this affects the subcortical masks in any (significant?) way.

What sort of differences should I expect between the masks in the

"freesurfer space" and the ones converted back to native space? Are there

any structures or artifacts I should mindful of?

Thank you!

Assaf

Just to make things concrete, assuming I have a patient called Sam, then, after

running recon-all, I typed in:

cd $SUBJECTS_DIR/Sam/mri

mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o brain-in-rawavg.mgz

mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz

e.g., for cerebral WM:

mri_extract_label aseg-in-rawavg.mgz 2 41 cerebralWMNative.mgh

mri_convert cerebralWMNative.mgh cerebralWMNative.img

(this last step is used to create ANALYZE format images which is the format

my code is already structured to read out)