they will process the input based on the file name extensions, the problem is that things (like mris_make_surfaces) expect certain files (like brainmask.mgz) to be in certain places. This is the advantage of the simplicity of a script like recon-all: it hides all the complexity from you. But the price of course is flexibility - if you start changing names it won't know where to find things.
Bruce
On Wed, 6 Sep 2006, Graham Wideman wrote:
Doug and Nick:
Thanks for the quick replies. Notes:
Doug wrote:
mri_convert orig.mgz orig.mgh
Ah, good to know, and lets you rename in the same step, so avoids collision.
At 9/6/2006 02:14 PM, you wrote: 1. You should keep the orig directory as that's where you store the the input data
Yep, I knew about that one :-)
Nick said:
Yes, freesurfer recognizes the filename extension .mgh (and just doesnt do the gunzip on it internally).
But Doug said: 2. I'm not sure that everything will run smoothly with mgh. I think a lot of stuff is hardcoded to work with mgz and/or COR
Hmmm, so not sure what to make of that. Ideally programs would process the input based on the filename extension, and then produce same-format output. But that may not have been a priority.
Graham