Hi Kasper, It should work (I tried it a while ago with the dev version and it did not crash :-). Could not really tell if it helped much either. I don't remember if functionality is available in FS5.3 to include that in a long run. In dev, you would include the T2 for both the cross and long run. The long run then takes the T2 from the cross. Not sure if it works passing it directly into a longitudinal run.
Best, Martin
On 05/13/2016 08:43 AM, Bruce Fischl wrote:
Hi Kasper,
I don't see why not, but we haven't done this yet I don't think, so there may be undiscovered bugs. Bruce On Fri, 13 May 2016, Kasper Jessen wrote:
Dear FreeSurfer, Currently, we have only manual edited the BASE (the CROSS was left unedited) in an longitudinal data. However, some cortical areas (f.eks. such as the inferior temporal area) are difficult to edit accurately due to image quality. I then read through the release notes (stable v5.2.0) and found that a T2/FLAIR can be used to improve the pial surface.
Question: Is it possible to use a T2 and run either -autorecon3 and -T2pial on the [LONG] runs to get extra improvement of the final pial surfaces?
Best regards, Kasper Jessen
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