Thanks. I've put code in the "empty" block, but this gives me two additional questions:
1) the align_epi_anat.py step fails when I feed it the fieldmap-corrected data (apparently because the file, in NIFTI format, does not have type "epi"). Is there any way I can make an AFNI header for this file that will contain the "type" attribute?
The error I get is:
**ERROR Could not square a circle (3dAllineate could not align anat to epi)
Traceback (most recent call last):
File "align_epi_anat.py", line 3016 in <module>
ps.align_anat2epi(e, a, ps.epi_wt, ps.AlOpt, suff, mcost)
TypeError: 'NoneType' object is not iterable
################################################
2) I'd like to do the fieldmapping before Talairaching, but it looks like the volreg step has to be done using Talairaching options. What I'd WANT to do is:
-blocks tshift volreg empty align mask blur scale regress tlrc
This allow me to do all processing in native space and then only tlrc at the end.
but what I think the script needed is:
-blocks tshift empty align tlrc volreg mask blur scale regress.
Is this correct?
--Matt
