Hi Bastian,

this is in cases where you need to make the images symmetric so that recon-all processing works, but then do the analysis on the original (non flipped) hemisphere in each subject. You should not use this to do a point wise comparison between left (original healthy) and flipped (right originally healthy) hemispheres, as you may introduce a bias. Freesurfer atlases are hemisphere specific.

Best, Martin

On 08/19/2014 01:51 PM, Martin Reuter wrote:
Hi Bastian,

yes, I have some code to do what you want. You would duplicate and flip the good hemisphere in the image and then run FS on the symmetric heads. This can be done via robust_register and (mis)-using the mid space.
You can find some description of this procedure here:
Robust and Accurate Contralateral Registration for Pose Normalization and Tumor Segmentation. M.Reuter, H.D.Rosas, B.Fischl. Human Brain Mapping 2012, Beijing.
http://reuter.mit.edu/blue/papers/reuter-hbm12-tumor/reuter-hbm12-tumor.pdf

and the mid-space registration is described here:
Highly Accurate Inverse Consistent Registration: A Robust Approach. M. Reuter, H.D. Rosas, B. Fischl. NeuroImage 53(4):1181-1196, 2010.
http://reuter.mit.edu/papers/reuter-robreg10.pdf

I currently cannot access the folder with the scripts, please send me an email directly ( mreuter@nmr.mgh.harvard.edu ) and I'll send it over as soon as I have access again.

Best, Martin


On 08/12/2014 02:56 AM, Bastian Cheng wrote:
Dear Freesurfers,

Has anyone accomplished analysis of longitudinal cortex changes in a
dataset with "flipped" hemispheres?

I am currently struggling with data from stroke patients, half of them
with lesions on the right, half of them on the left side of the brain.

What I am planning: flip all healthy hemispheres to left and perform
longitud. analysis of cortical thickness change on that (helthy)
hemisphere.

I have read the notes on Surface-based Interhemispheric Registration
(xhemi) and most of the comments here. It seems to me that this would
allow me to compare both hemisph. sides at ONE timepoint. (but not
actually analyzing ONE (flipped) hemisphere over time).

Any help to point me in the right direction is greatly appreciated!

Bastian
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer






_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer