Closed dlevitas closed 4 years ago
Hi @dlevitas , Thanks for opening this issue and offering your help. Pydeface uses FLIRT from FSL to linearly register input images to a template image. I think this step takes the most amount of time during defacing. I can think of the following to speed it up:
--template
and --facemask
flags.--cost
options.These being said, I think speeding up pydeface is not a high priority issue as long as it is accurate enough and fast enough at the same time (e.g. not taking a day for defacing one image) while staying easy to install.
Thanks @ofgulban. I'll look into these options but try to avoid deviating too far from pydeface's defaults, which have worked extremely well for me in the past.
Hello,
I'm defacing my anatomical data using version 2.0, and have noticed on different datasets that the defacing can take anywhere from 2-3 minutes for some anatomical images, to 8-10 minutes for others. Other than potential data quality issues, such as motion artifacts and/or poor CNR, are there other factors that can increase the time, such as slow HPC I/O? I'm trying to see if there is anything I can do to reduce the time.
Thanks!