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

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Antonio Gisbert
October 21, 2008 10:01AM
Hello,

I've been running into two problems while trying to use align_epi_anat.py (v1.12). It might just be a usage issue.

1. align_epi_anat.py -anat anat_raw+orig.HEAD \
-epi run4_raw+orig.HEAD -epi_base 253 -child_epi run?_raw+orig.HEAD \
-epi2anat

Creates the appropriate run4_raw_al+orig files but does not generate the other run[123]_raw_al+orig files. It does, however, create run[123]_raw_al_reg_mat.aff12.1D files, which I believe I should be able to use to generate *_al_orig files. How?

2. align_epi_anat.py -anat anat_raw+orig.HEAD \
-epi run4_raw+orig.HEAD -epi_base 253 -child_epi run?_raw+orig.HEAD \
-volreg on -volreg_opts -1Dfile motion -epi2anat

Creates a run[123]_raw_motion.1D file but does not generate the other run[123]_raw_motion.1D files. I need these files for 3dDeconvolve, how can I get them?

Many thanks,

Antonio

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Subject Author Posted

align_epi_anat.py help

Antonio Gisbert October 21, 2008 10:01AM

Re: align_epi_anat.py help

Daniel Glen October 21, 2008 01:10PM

Re: align_epi_anat.py help

Antonio Gisbert October 21, 2008 04:05PM