I took a look at the xhemireg script and I feel like editing this to serve my purposes might be too tall of an order.

However, I think I have a processing stream that will work — I want to make sure there’s nothing problematic about it.

1. Run recon-all on the properly oriented T1 images through -segmentation

2. Take the old hand-edited wm.mgz file [containing extensive hand-edits] and left/right flip this file (using mri_convert to change LIA to RIA)

3. Visually confirm alignment of this hand-edited, flipped wm.mgz file. It turns out this brain was shifted by 1 voxel in the left/right direction; I manually adjusted this after converting the file to COR-format, and then converted back to .mgz and visually confirmed proper alignment.

4. Drop this hand-edited, L/R flipped and 1-voxel-shifted wm.mgz file into the subject/mri directory from running recon-all in (#1), then proceed with recon-all -autorecon2-wm -autorecon3

Is there anything inherently flawed about this approach? Are there any other files that I also need to flip (i.e., wm.seg.mgz or anything else?)

thanks,

Dan

On 4/17/17 6:48 PM, Douglas Greve wrote:

you can try xhemireg. it is kind of meant to do this kind of thing, but 
not to the extent that you need it. If you know a little programming, 
you can try to edit the script so that it does everything.


On 4/17/17 6:43 PM, Dan Grupe wrote:
> Hi all,
>
> After running a bunch of subjects through FreeSurfer and making 
> extensive manual edits to the white matter masks, we discovered that 
> the data were left/right flipped during the dicom-to-nifti conversion 
> process. I hope to maintain these manual edits while processing data 
> in the proper orientation and running them through the rest of the 
> pipeline. Is this possible to do?
>
> An old thread from 10 years ago directed me to this page: 
> https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal that 
> offered some tips on how to go about this. However, after confirming 
> that the volume was reversed running recon-all -autorecon1 in a new 
> directory, I encountered an error message:
>
> > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm 
> ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)
>
> This problem does not arise when running the same command on a copy of 
> this subject’s non-flipped data.
>
> Are there different steps that I should be following to rectify the 
> problem? Or can you help me troubleshoot this error?
>
> Best,
> Dan