This page describes the steps taken to Left-Right reverse a subject in order to validate that there was a RH dominant asymmetry in the hippocampal volumes and not a bias introduced by the segmentation atlas.

To Left-Right reverse your subject:

(all commands run from within your subjects mri/ subdirectory)

First you need to get the orientation string of the volume:

mri_info --orientation orig.mgz

This will return either LIA or RIA. Then run mri_convert with that orientation string, but changing L to R:

mri_convert --in_orientation RIA orig.mgz orig.lrflipped.mgz

You can check visually to see that these two volumes are actually a reversal of each other:

tkmedit -f orig.mgz -aux orig.lrflipped.mgz

When you are satisfied that you have a reversal you should make a new subject directory within your SUBJECTS_DIR and copy this reversed volume in as the new subject's orig volume:

mkdir -p $SUBJECTS_DIR/LRflipped-subject/mri
cp orig.lrflipped.mgz $SUBJECTS_DIR/LRflipped-subject/mri/orig.mgz

Launch recon-all as normal, running only through the skull strip:

recon-all -autorecon1 -nomotioncor -s LRflipped-subject

*the -nomotioncor flag is used because we've copied in an orig, but have not 001 volume.

>>>> 1. I made a copy of the original subjects 010103_61864 and >>>> 030324_vc11522 , called orig_010103_61864 and orig_030324_vc11522 >>>> (just to be sure I didn't write over anything or mess it up!) 2. I >>>> then LR reversed them and called those subjects >>>> LR_flipped-010103_61864 and LR_flipped-030324_vc11522 3. I've >>>> checked them visually to make sure they are a LR reversal of the >>>> original subjects. >>>> 4. I converted the appropriate volumes (brainmask.mgz, nu.mgz) to >>>> COR and edited the COR-.info file to remove the RAS coordinate >>>> transformation which was hindering the LR reversal. >>>> 5. On ALL of these subjects (orig and LR_flipped) I ran the aseg >>>> that is in stable3 to get hippocampal volumes. >>>> >>>> Here are the numbers: >>>> orig_010103_61864: >>>> Left-Hippocampus_vol = 2627.0 >>>> Right-Hippocampus_vol = 3195.0 >>>> orig_030324_vc11522: >>>> Left-Hippocampus_vol = 3137.0 >>>> Right-Hippocampus_vol = 3771.0 >>>> **orig volumes show a RH dominant asymmetry >>>> >>>> LR_flipped-010103_61864: >>>> Left-Hippocampus_vol = 3023.0 >>>> Right-Hippocampus_vol = 2688.0 >>>> LR_flipped-030324_vc11522: >>>> Left-Hippocampus_vol = 3685.0 >>>> Right-Hippocampus_vol = 3218.0 >>>> **LR_flipped volumes show a LH dominant asymmetry >>>>