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?

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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