Hi,

Just this week I've started to try to use align_epi_anat.py to try to preprocess and talairach oblique epi data (with -tlrc_apar). I've run into trouble whenever using the default anat2epi option. Whereas the -epi2anat option works fine, the default -anat2epi option only creates an aligned anat file, but no epis. Looking at the __tt_* temp files (using -keep_rm_files), it seems to be the case the script dies at some point during the epi preprocessing; it seems to be when it tries to time-shift the child epi, for what that's worth. This is before either the base or the child epis are talairached.

However, as I said earlier, these very same epi files are preprocessed just fine if you align them to the anat instead of aligning the anat to the epis, so it doesn't seem like there's a general problem with my particular epi files.

Here's the script invocation -- it's totally generic:

align_epi_anat.py \
-anat anat+orig \
-epi epi_r1+orig \
-epi_base 0 \
-anat2epi \
-big_move \
-child_epi epi_r2+orig \
-tlrc_apar anat_at+tlrc

So to reiterate, this would bomb out eventually, whereas if I just replace -anat2epi with -epi2anat, the script works fine, albeit with the opposite direction of alignment.

I've tried this without the -big_move option, and also with the newer -giant_move option, but none of them work any better.

I was somewhat surprised that the script just seems to end happily without indicating that it failed in any way, even in it's most verbose mode... It creates the anat_al+orig file just fine, and that looks to be perfectly aligned with my oblique epis. So there's no failure to align due to the obliqueness of the epi. But then the script never makes it through the full epi preprocessing (slice-time correction, motion correction, talairaching). And then it proceeds to delete all of the temp files (including some potentially useful preprocessed epis).

Any thoughts? Is this script working just fine for everyone else? Could my problem be related to the one that Iris Yang recently reported?

Thanks,
Leigh