Hi gurus,

I've been having a couple of issues with align_epi_anat.py recently. The first issue is that the script crashes when I try to run it on EPIs that are not in the current directory. The temporary and output files are getting created in the current working directory (which is where I want them, and where fresh_start() looks for them), but the script subsequently searches for them in the directory in which the EPIs reside. The crash, after I've inserted some debugging statements into the script, looks like this:

#++ align_epi_anat version: 1.35
#++ turning off volume registration
#Script is running:
  3dAttribute DELTA /study/fmfmri/data/processed/016/epis/warm_cdmf+orig
#Script is running:
  3dAttribute DELTA /study/fmfmri/data/processed/016/epis/warm_cdmf+orig
#Script is running:
  3dAttribute DELTA /study4/fmfmri/data/processed/016/anat/T1High_ns+orig
#++ Multi-cost is lpc
name = opt.parlist[0] = /study/fmfmri/data/processed/016/epis/warm_cdmf+orig[0]
rp = os.path.dirname(name) = /study/fmfmri/data/processed/016/epis
ap = os.path.abspath(rp) = /study/fmfmri/data/processed/016/epis
e.path = /study/fmfmri/data/processed/016/epis/
e.prefix = warm_cdmf
os.getcwd() = /study4/fmfmri/data/processed/016/anat
e.ppv() = /study/fmfmri/data/processed/016/epis/warm_cdmf+orig
e.out_prefix() = warm_cdmf
#++ Removing all the temporary files
#Script is running:
  \rm -f __tt_warm_cdmf*
#Script is running:
  \rm -f __tt_T1High_ns*
#Script is running:
  3dcopy /study4/fmfmri/data/processed/016/anat/T1High_ns+orig __tt_T1High_ns
++ 3dcopy: AFNI version=AFNI_2011_12_21_1014 (Aug 15 2012) [64-bit]
#Script is running (command trimmed):
  3dinfo ./__tt_T1High_ns+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique'
#++ Dataset /study4/fmfmri/data/processed/016/anat/__tt_T1High_ns+orig is not oblique
#Script is running:
  3dinfo /study/fmfmri/data/processed/016/epis/warm_cdmf+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique'
#++ Dataset /study/fmfmri/data/processed/016/epis/warm_cdmf+orig is not oblique
e.path = /study/fmfmri/data/processed/016/epis/
e.prefix = warm_cdmf
e.view = +orig
e.type = BRIK
os.getcwd() = /study4/fmfmri/data/processed/016/anat
e.p() = /study/fmfmri/data/processed/016/epis/
#++ Creating representative epi sub-brick
#Script is running:
  3dbucket -prefix __tt_warm_cdmf_ts /study/fmfmri/data/processed/016/epis/warm_cdmf+orig'[0]'
++ 3dbucket: AFNI version=AFNI_2011_12_21_1014 (Aug 15 2012) [64-bit]
o.out_prefix() = __tt_warm_cdmf_ts
o.ppv() = /study/fmfmri/data/processed/016/epis/__tt_warm_cdmf_ts+orig
o.exist() = 0
** ERROR: Could not 3dTstat epi
#++ resampling epi to match anat data
Traceback (most recent call last):
  File "/home/schwabacher/afni_src/python_scripts/align_epi_anat.py", line 3035, in <module>
    ps.process_epi(use_ss=ps.epi_strip_method)
  File "/home/schwabacher/afni_src/python_scripts/align_epi_anat.py", line 2751, in process_epi
    e = self.resample_epi( o,"", prefix)
  File "/home/schwabacher/afni_src/python_scripts/align_epi_anat.py", line 2542, in resample_epi
    % (ps.anat_ns.input(), o.out_prefix(), e.input(),sb), ps.oexec)
AttributeError: 'NoneType' object has no attribute 'input'

I think that changing various

o = e.new(prefix)

to

o = afni_name(e.out_prefix()).new(prefix)

should fix this, though I'm not entirely sure because I got a little lost among the 'e's, 'o's and 'a's.

The other issue is that align_epi_anat.py for some reason just discards any selectors attached to its input, which I traced to the fact that it uses afni_name.input(self), which has this behavior. I assume this is this way because otherwise the world would break, but it would be nice if it worked the same as the other programs. It took me a while to figure out why it was taking so long to generate a high-resolution version of the high-contrast frame of my EPI data for quality checking purposes!

Isaac



Edited 1 time(s). Last edit at 10/08/2012 06:37PM by Isaac Schwabacher.