search

nipy / mindboggle

Automated anatomical brain label/shape analysis software (+ website)
http://mindboggle.info
Other
143 stars 54 forks source link

include recon-all's 3T flag #121

Closed PeerHerholz closed 7 years ago

PeerHerholz commented 7 years ago

I really like the easy and comfortable application of mindboggle123. However, maybe some users would like to include recon-all's 3T flag when calling the pipeline!?

PeerHerholz commented 7 years ago

Hey,

as I just have my laptop with me and no remote access to my system at home, I only started the script to check the recon-all log. As far as I can tell all specified flags are passed correctly. Sorry for the inconvenience. Additionally, my implementation appears to be quite hacky, but I wasn't sure how to do it otherwise. If someone has a smoother solution, that would be great. Thx @spam-depository for also having a look on it.

binarybottle commented 7 years ago

Thank you, @PeerHerholz! @satra -- would you prefer that the --fs_T2image flag be absorbed into the more general flag, or be kept separate? Do these changes work for you?

satra commented 7 years ago

@binarybottle - i would keep the T2image flag separate - it doesn't fit into this implementation and also involves pointing to a location within the container.

satra commented 7 years ago

@binarybottle - a minor release would be good.