**Sending this again because it never showed up on the mail archive.
Hi Doug,
I ran it again with —debug as the first argument as you suggested and have attached the terminal output. Thanks for your help. We are quickly approaching a deadline to get this figured out so we greatly appreciate your help! Thank you so much!
The thread is confusing so, I included previous messages below, just in case. I am never able to keep the thread together for some reason.
Best, Sherryse ________________________________ Douglas N Grevehttp://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+N+Greve%22 Tue, 27 May 2014 15:46:24 -0700http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20140527
recon-all will not produce the registration file you are looking for. It should be produced by reg-feat2anat. Try running it with --debug as the first argument and post the terminal output to the list doug
________________________________ Bruce Fischlhttp://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Bruce+Fischl%22 Fri, 30 May 2014 12:53:23 -0700http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20140530
Hi Sherryse
mostly I'll leave this for Doug. Have you tried using bbregister directly? It might be embedded within reg-feat2anat, I'm not sure
Bruce
________________________________
Thanks Bruce. The problem is that the registration itself is not working
properly.
Recap: The goal is to view the functional data on the inflated brain. We ran recon-all, checked that registration, then attempted to register the functional data to the free surfer anatomical. My understanding is that running reg-feat2anat should create a folder (featdir/reg/freesurfer) with register.dat and anat2exf.register.dat files in (among others). The folder is created and some of the files are created, but those two are not.
Although, I should note that there is a file created within this folder called anat2exf.register.dat.init. But I am not sure what the ³init² is for or what it means.
The terminal output from running reg-feat2anat is attached. I can see now that there are errors in the output (I am slowly figuring how how to use FreeSurfer!).
Any suggestions you have are greatly appreciated! Thanks!
Sherryse
-- Sherryse Corrow, Ph.D. / Postdoctoral Fellow Human Vision and Eye Movement Lab Department of Ophthalmology & Visual Sciences UBC/VGH Eye Care Centre 360A-2550 Willow Street Vancouver, BC, V5Z 3N9 Tel: 604-875-4111 ext 67672 Cell: 604-315-6717 sherryse.corrow@eyecarecentre.orgmailto:sherryse.corrow@eyecarecentre.org