This is a follow up to Lisa's problem. We've tried a newer version of afni (AFNI version=AFNI_2011_12_21_1014 (May 3 2012) [64-bit]) and still get the error. The issue has to do with 3dRefit not being able to overwrite a file when it is called by @auto_tlrc. Running 3dRefit on the command line seems to be fine. Trying a number of configurations, I found that the issue is related to having a system wide afnirc file and setting the AFNI_DECONFLICT variable to NO.

Here is a table of the observed behavior:

Note: we have a system wide file (AFNI_SYSTEM_AFNIRC=/etc/afni/afnirc), and a personal .afnirc file.

I've varied whether the files exist, have AFNI_DECONFLICT set to NO and AFNI_DECONFLICT set to OVERWRITE. Whether the variable is set in the shell or not does not seem to affect the behavior.

/etc/afni/afnirc (does not exist)
.afnirc (does not exist)
@auto_tlrc works

/etc/afni/afnirc (does not exist)
.afnirc (AFNI_DECONFLICT = OVERWRITE)
@auto_tlrc works

/etc/afni/afnirc (does not exist)
.afnirc (AFNI_DECONFLICT = NO)
@auto_tlrc works

/etc/afni/afnirc (AFNI_DECONFLICT = OVERWRITE)
.afnirc (does not exist)
@auto_tlrc works

/etc/afni/afnirc (AFNI_DECONFLICT = OVERWRITE)
.afnirc (AFNI_DECONFLICT = OVERWRITE)
@auto_tlrc works

/etc/afni/afnirc (AFNI_DECONFLICT = OVERWRITE)
.afnirc (AFNI_DECONFLICT = NO)
@auto_tlrc does not work

/etc/afni/afnirc (AFNI_DECONFLICT = NO)
.afnirc (does not exist)
@auto_tlrc does not work

/etc/afni/afnirc (AFNI_DECONFLICT = NO)
.afnirc (AFNI_DECONFLICT = OVERWRITE)
@auto_tlrc works

/etc/afni/afnirc (AFNI_DECONFLICT = NO)
.afnirc (AFNI_DECONFLICT = NO)
@auto_tlrc does not work

-Colin