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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September 15, 2018 09:33AM
Hi rick,
I don't find any slice timing information in HEAD file, so I should use '-tpattern'.
However, I have two kinds of slice orders in experiment. In the first four runs, the slice order is 2, 4, 6, 8, ......,30, 32,1, 3, 5, 7,......,29,31; and in the back four runs, the slice order is 31,29,27,25,....3,1,32,30,28,26,......4,2.
The script is
#!/bin/tcsh
afni_proc.py -subj_id cl \
-dsets cl_epi_r??+orig.HEAD \
-blocks tshift align volreg blur \
-copy_files slice_times.1D \
-copy_anat cl_anat+orig \
-tshift_opts_ts -tpattern @slice_times*.1D \
-volreg_base_dset ${sid}_loc_r1+orig'[0]' \
-blur_size 4.0

I don't know how to extract the first slice timing file automatically in the first four runs, and how to extract the second slice timing file automatically in the back four runs in script.
Thanks a lot!

jiaxin
Subject Author Posted

NII to BRIK questions

Nathan Petro September 12, 2018 04:04PM

Re: NII to BRIK questions

rick reynolds September 13, 2018 09:13AM

Re: NII to BRIK questions

jiaxin September 15, 2018 03:38AM

Re: NII to BRIK questions

jiaxin September 15, 2018 09:33AM

Re: NII to BRIK questions

Peter Molfese September 13, 2018 10:10AM

Re: NII to BRIK questions

Nathan Petro September 26, 2018 04:16PM