If you have a registration matrix that maps to the desired orientation,
then you can apply it to a segmentation with mri_label2vol. But why not
just register the anatomical to the DTI (bbregister) and then run
mri_label2vol with that registration to map the WM mask directly into
the native DTI space?
On 7/25/16 7:56 AM, Sandra Hanekamp wrote:
Dear Freesurfer community,
I would like to apply ACPC alignment to Freesurfer output.
Data was previously segmented with recon -all and a lot of manual
editing using ITK. Unfortunately, the data was not aligned to ACPC and
this causes errors in my pipeline (I am using the labels and white
matter mask from Freesurfer for my DTI analysis).
Re-doing the segmentation plus necessary edits would be very
time-consuming due to a poor contrast between white and grey matter
and the number of scans that I have, so I would prefer to align the
current output to ACPC. Does anyone know a solution that does not
involve re-doing the segmentation? How can I apply ACPC alignment to
Freesurfer output?
Thank you so much for any thoughts or recommendations you might be
able to provide.
Sandra Hanekamp
Laboratory for Experimental Ophthalmology
University Medical Center Groningen
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