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  

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August 08, 2013 04:10AM
ah ok, I didn't know align_epi_anat.py already concatenates the matrices automatically.

I adjusted the code below, sot that the Allineate calculcation is only done on the sub-brick #0 of the source. Since I already use volreg for motion correction, I think it would be a bit double-stitched (and extremely slow) to run allineate also on every repetition.

3dTcat -prefix first_only_$subj pb00.$subj.r$run.tcat+orig'[0]'
align_epi_anat.py -dset2to1 -dset1 ../TEMPLATE+orig -dset2 first_only_$subj+orig 	\
		  -child_dset2 pb00.$subj.r$run.tcat+orig				\
		  -big_move								\
		  -volreg on -volreg_method 3dvolreg					\
		  -volreg_opts '-Fourier -zpad 1'					\
		  -AddEdge -dset1_strip None -dset2_strip None				\
		  -Allineate_opts '-twofirst -twoblur 0.8 -source_automask+1'		\
		  -tshift on -tshift_opts -tzero 0 -quintic				\
		  -AddEdge								\
		  -dset2_base 0								\
		  -volreg_base 0							\
		  -cost lpa

...still checking the results



Edited 5 time(s). Last edit at 08/08/2013 05:23AM by paranoidandroid.
Subject Author Posted

My coregistration code needs some suggestions for improvement

paranoidandroid August 07, 2013 01:02PM

Re: My coregistration code needs some suggestions for improvement

Daniel Glen August 07, 2013 01:45PM

Re: My coregistration code needs some suggestions for improvement

paranoidandroid August 08, 2013 04:10AM