Hi Ruthger,
I've only tested the deformation on T2-space, and mostly with a flair inversion pulse, so it is probably the case that it doesn't work well with your sequence. If you want to upload the data I'll try to take a look, but it probably won't be soon
sorry Bruce
On Mon, 14 Apr 2014, Righart, Ruthger wrote:
Dear Freesurfers,
I have run several subjects using the -T2pial flag, to correct for dura. For several subjects the pial surface was badly positioned after the -T2pial flag was used (these errors did not occur when the flag was not used, in the same subject, see PDF, left vs right panel).
I was wondering if adding this flag might be problematic in some patient groups, like cerebrovascular disease or multiple sclerosis, with regard to T2 (hyperintense) lesions.
Best, Ruthger