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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
