I want to average multiple structural scans for input into the surface recon. Two are axial and one is sagittal. (I plan to correct for the gradient inhomogeneities in the sagittal images, so that shouldn't be an issue.)
Anyway, the problem comes when recon-all does "motion correction" to align the scans. For some strange reason, the axial and sagittal scan protocols use slightly different TRs and TEs (e.g. TR=7.996 vs. 8.012). For some even stranger reason, this brings recon-all to a screaching halt. I'm guessing that this is actually a MINC problem but I wonder if there is a way to make it ignore the TR and TE when aligning two structural scans.
My work around is to explicitly set the TR and TE for the sagittal scan when running mri_convert: mri_convert -tr 8.012 -te 3.136 -it dicom i*.1 $destdir/$mgzname.mgz