Hi there,

I am using align_api_anat.py under afni_proc.py for some alignment of epi (partial coverage) to an anatomical

I am getting some warnings with my first pass (code below), and just wanted to make sure I am doing the right things.

The first warnings are about obliquity.

I get obliquity warnings about my epi (around 36 degrees from plumb) during most parts of the processing (3dToutcount, 3dAutomask, 3drefit, 3dAllineate etc.)
I also get two obliquity warnings about my anatomical (about 2 degrees from plumb) during 3dAutomask and 3dAllineate

The anatomical warning is a bit weird because 3dinfo says it is not oblique at one point in the output:

3dinfo ./__tt_FR_uniden_avg_ns+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique'
#++ Dataset /scratch/inode/uqhdemp1/P007_playing/P007_FR_6.results/__tt_FR_uniden_avg_ns+orig is not oblique
#Script is running (command trimmed):
3dinfo ./pb00.P007_FR_6.r01.tcat+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique'
#++ Dataset /scratch/inode/uqhdemp1/P007_playing/P007_FR_6.results/pb00.P007_FR_6.r01.tcat+orig is ***oblique****

From what I can tell, because I am using align_epi_anat.py, it works out I have obliquity and includes this in the alignment. I can see obliquity transformation in the output for 3dAllineate.
Q: is it dealing with the obliquity, so I don't need to worry/ do anything further?
Q: Does it deoblique the epi, or the anatomical, or just aligns them to each other so you don't need to worry about obliquity?

In a later round of processing, I included -deoblique as an option in align_epi_anat.py (see second pass code), but I still get the warnings.
Q: Do I need to bother including this -deoblique if it is seemingly doing it anyway in align_epi_anat.py?

[I am aware I can turn the warnings off if I like by editing my .afniric file]
[Alignments appear to be good - and no difference with -deoblique on or not specified from what I can tell visually]
[I am aware they are just warnings, not errors]



The second warnings are about autoweight

I have not specified my cost function in align_epi_anat.py and seems to be using the default -lpc. I get the following warning about using autoweight

'-autoweight' is recommended when using -lpc or -lpa #
++ # If your results are not good, please try again

The info in 3dAllineate -help looks like you need to specify numbers to say how you want the autoweight to be computed...? I don't really know what I should be doing here, so would not know what numbers to specify...

I tried putting -autoweight on its own as an option in align_epi_anat (see third pass code below) but does not run (brings up an error).
Q: I guess my question is, should I be using autoweight? If so, how do I add it as an option?



The third warning was about cmass

My align_epi_anat produces three 3dAllineate blocks
- The first is e2a alignment only, this appears to use cmass+a
- The second combines e2a and oblique transformations to make my new warped anatomical without skull --> this is where I get the following warnings

[7m*+ WARNING: [0m center of mass shifts (-cmass) are turned off, but would be TERRIBLY large!
[7m*+ WARNING: [0m - at least one is more than 50% of search range
...
[7m*+ WARNING: [0m -cmass was turned off, but might have been needed :(
please check your results - PLEASE PLEASE PLEASE

Q: Do I need to add cmass option into my code? (presumably cmass+a if do, due to partial volume)
Q: I tried putting the option in as -cmass+a but this did not work, so I put -cmass cmass+a (see fourth pass code). Is this wrong?

[Note: I ran the third pass code and still get warnings about cmass being turned off in the second 3dAllineate...]
[Also, the help options suggest I am already getting cmass shifts with ginormous_move, which might be why I see cmass+a in the first 3dAllineate block... so maybe I don't need to change anything?]


Sorry about having so many questions, I am a major noob to all things fMRI. This is literally my first analysis :o

Thank you for your time,

Harriet



------------------------

First pass code.

afni_proc.py -subj_id $subj \
-blocks align \
-dsets $data_dir/P007_FR_RUN* \
-tcat_remove_first_trs 0 \
-copy_anat $data_dir/FR_uniden_avg \
-anat_has_skull yes \
-align_opts_aea \
-ginormous_move \
-partial_coverage


-----------------

Second pass code

afni_proc.py -subj_id $subj \
-blocks align \
-dsets $data_dir/P007_FR_RUN* \
-tcat_remove_first_trs 0 \
-copy_anat $data_dir/FR_uniden_avg \
-anat_has_skull yes \
-align_opts_aea \
-deoblique on \
-ginormous_move \
-partial_coverage


------------------------------

Third pass code
afni_proc.py -subj_id $subj \
-blocks align \
-dsets $data_dir/P007_FR_RUN* \
-tcat_remove_first_trs 0 \
-copy_anat $data_dir/FR_uniden_avg \
-anat_has_skull yes \
-align_opts_aea \
-deoblique on \
-ginormous_move \
-partial_coverage \
-autoweight


------------------------------

Fourth pass code
afni_proc.py -subj_id $subj \
-blocks align \
-dsets $data_dir/P007_FR_RUN* \
-tcat_remove_first_trs 0 \
-copy_anat $data_dir/FR_uniden_avg \
-anat_has_skull yes \
-align_opts_aea \
-deoblique on \
-ginormous_move \
-partial_coverage \
-cmass cmass+a