Hi, Ann-

What is your AFNI version ("afni -ver")?

One first thing to note about your afni_proc.py command the QC: using "-html_review_style pythonic" will give you much nicer looking line plots (assuming you have Python plus the Matplotlib module installed on your computer). You can re-run the APQC in pythonic-mode once we sort the other issue(s), without having to rerun the full afni_proc.py. At the moment, the way to do this would be to run:

wget [github.com]

... to download a file (that I should just add to the distribution). After that, you can run:

tcsh redo_apqc.tcsh AP_RESULTS_DIR

... where AP_RESULTS_DIR is a list of one or more results directory locations; this program will push any existing QC_${subj} dir to QC_${subj}_TIMESTAMP and create a new one.

Re. Q3 (because you did sneak a third question in!):
Adding these lines in won't do anything for your code here:

-tlrc_NL_warped_dsets anatQQ.FT.nii anatQQ.FT.aff12.1D  anatQQ.FT_WARP.nii

... because these are for when you run a program called "@SSwarper" before afni_proc.py to do a combined skullstripping (SS) and nonlinear alignment (warping) to a template from your anatomical T1w volume. This program is run *before* afni_proc.py, and then you pass the results of the warping into the program---this line that you have highlighted passes the results in.

The benefit of using @SSwarper first is that 1) it tends to provide the best nonlinear alignment and skullstripping, and 2) you can check the results and re-run that part of the processing if necessary separate from the rest of things. Nonlinear warping can be slow, so doing this ahead of time is nice in case you decide to re-run afni_proc.py with other settings---you don't have to re-do the nonlinear alignment part.

In your case, you could run this program as follows (not the different MNI template: @SSwarper requires a special, multi-brick version of the MNI template, which we distribute, more info here, if you are interested: [afni.nimh.nih.gov]):

@SSwarper                                     \
        -tmp_name_nice                            \
        -input   $sdir/${anatsubj}_SurfVol+orig                  \
        -base    MNI152_2009_template_SSW.nii.gz  \
        -subid   ${subj}                          \
        -odir    group/o.aw_${subj}

... The @SSwarper help tells you how to provide this info to afni_proc.py, then. Some pieces are:

    -copy_anat group/o.aw_${subj}/anatSS.${subj}.nii                               \
     -anat_has_skull no                                          \
....
      -volreg_tlrc_warp -tlrc_base MNI152_2009_template_SSW.nii.gz           \
....
      -tlrc_NL_warp                                               \
      -tlrc_NL_warped_dsets                                       \
         group/o.aw_${subj}/anatQQ.${subj}.nii                                       \
         group/o.aw_${subj}/anatQQ.${subj}.aff12.1D                                  \
         group/o.aw_${subj}/anatQQ.${subj}_WARP.nii

... where the exact paths might change.

Re. Q1: There should be a file called "out.review_html" in your *.results directory from afni_proc.py. That contains a log of all the APQC (afni_proc.py QC) generation. Could you email me that?

Re. Q2: That Xmat failure is odd... I am not sure---that is probably a Rick-level question, and I will ping him.

--pt