AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

Previous Message Next Message
Message List New Topic Print View
|
nicreap
December 29, 2014 11:19AM
With the 3dWarp step it is
3dWarp -card2oblique 9518_run_1+orig. -prefix 9518_avg_obl_anat 9518_avg_anat+orig.
followed by

align_epi_anat.py -epi2anat -tshift off -epi_base 0 -skullstrip_opts -no_use_edge -anat 9518_avg_obl_anat+orig -epi 9518_run_1+orig
-child_epi 9518_run_02+orig 9518_run_03+orig 9518_run_04+orig

When I run it without the 3dWarp it is

align_epi_anat.py -epi2anat -tshift off -epi_base 0 -skullstrip_opts -no_use_edge -anat 9518_avg_anat+orig -epi 9518_run_1+orig
-child_epi 9518_run_02+orig 9518_run_03+orig 9518_run_04+orig

I am not sure if it makes a difference but we did clustered acquisition for our datasets, so there is an acquisition, then roughly 10 seconds of off time and then another acquisition.

Thanks for your assistance, if you need anything else let me know.
Reply Quote
RSS
Subject Author Posted

Trouble with Oblique datasets

nicreap December 23, 2014 02:20PM

Re: Trouble with Oblique datasets

Peter Molfese December 23, 2014 04:27PM

Re: Trouble with Oblique datasets

nicreap December 29, 2014 11:19AM

Re: Trouble with Oblique datasets

nicreap January 07, 2015 12:05PM

Re: Trouble with Oblique datasets

Peter Molfese January 07, 2015 01:42PM

Re: Trouble with Oblique datasets

nicreap January 07, 2015 03:22PM

Re: Trouble with Oblique datasets

Peter Molfese January 09, 2015 11:09AM

Re: Trouble with Oblique datasets

AjaySK January 06, 2015 03:43PM

Re: Trouble with Oblique datasets

Daniel Glen January 06, 2015 05:11PM