Difficulty with align_epi_anat


I would like to align my epi image to tlrc space. I first ran the following command to align the T1 to the atlas TT_N27:

@auto_tlrc -base TT_N27+tlrc -input subj_T1+orig

This produced a subjc_T1+tlrc BRIK and HEAD file. I then ran the following command:

-anat subj_T1+orig
-epi subj_epi+org
-epi_base 63
-tlrc_apar subj_T1+tlrc
-tshift off
-save_vr \

I get an error that it can’t open the dataset subj_T1_tlrc_al+tlrc+tlrc
I don’t understand why it’s looking for a file name with that many suffixes? What am I doing wrong in setting up the command?

Thanks so much for your help!!

Thanks for letting us know. I think I’ve fixed this now, and it’s in our git repository.

Thanks, Forgive me but I’m not super familiar with Git. How do I get the update from the git repository and integrate it with the existing afni version I have locally installed on my server?

Typically, most users don’t get the AFNI source code from git directly-- you would then have to compile it on your own computer to get executable “binary” programs (for the C ones, that is; the python and tcsh scripts would be executable directly). And it is not impossible to build AFNI on your own computer, it would just take users a little time and more installation.

We keep a git repo of the latest code, and then perform builds from time to time to compile all the C codes, so that when a user downloads AFNI, they get the latest version for their OS; of, if they have AFNI, then they can run a command which will: see if a newer version of compiled (=“built”) AFNI is available, and if so, get it and put it into the same location as their current AFNI binary directory. So, assuming you have AFNI on your computer at this moment, likely all you need to do to update your AFNI is run the following in your terminal:

@update.afni.binaries -d

Daniel’s mention of the git repo means that: an update has been made in the codebase, but probably we haven’t done a new build yet, so it isn’t available to The World by the “@update.afni.binaries -d” command yet. It will be soon; we tend to build fairly often with minor fixes+updates.