Dear all,
There seem to be some serious issues with the T2pial / FLAIRpial processing options provided in the latest versions of FreeSurfer.
First of all, although not clearly documented, T2pial / FLAIRpial processing does require the FSLDIR to be set (in order to use bbregister with --init-fsl). If not set, recon-all will finish just without using the T2 or FLAIR information. Importantly, no clear warning about this is given although the user expects that T2/FLAIR has been used for pial surface refinement. I think this is a very easy source of errors, so it might be a good idea to just throw an error when FSLDIR is missing and T2pial/FLAIRpial processing is requested.
Second, if FSLDIR has been set. T2pial/FLAIRpial uses bbregister with FLIRT initialisation to align the T2 or FLAIR image to orig.mgz. However, we have some high-res 3DFLAIR data in which this registration (more specifially, the FLIRT initialisation step of bbregister) seems to fail in more than half of the cases. Apparently, the FSL initialisation is not capable to change the orientation such that it fits to the coordinate system used for orig.mgz. Again, no warning or error is thrown, but the processing just continues with the wrong registration and without noticing the results will get worse compared to not using T2 or FLAIR. Although I know its essential to look at the output data; would it be possible to put some effort in letting the user know that things got wrong?
As a sidenote; I tried to fix this registration issue, but it seems to be very complicated using bbregister (other than just inserting my own registration obtained by using FLIRT to register native FLAIR to native T1, and subsequently transform the result to Freesurfer space in order to obtain FLAIR.mgz).
Best, Martijn