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
Dan Grupe, Ph.D. Assistant Scientist Waisman Laboratory for Brain Imaging and Behavior and Center for Healthy Minds University of Wisconsin-Madison
grupe@wisc.edu mailto:grupe@wisc.edu 608-263-7572 http://brainimaging.waisman.wisc.edu/~dgrupe
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