apqc_make_tcsh.py error


I am also getting this error for our VIA task when running the afni_proc.py from here.

if ( -e @ss_review_basic ) then
tee out.ss_review.9835MMH.txt
apqc_make_tcsh.py -review_style pythonic -subj_dir . -uvar_json out.ss_review_uvars.json
Traceback (most recent call last):
  File "/opt/afni/23.3.05/apqc_make_tcsh.py", line 459, in <module>
    cmd      = lat.apqc_vorig_all( ap_ssdict, obase, "vorig", "EPI", 
  File "/opt/afni/23.3.05/afnipy/lib_apqc_tcsh.py", line 2116, in apqc_vorig_all
    lll    = com.so[0].split()
IndexError: list index out of range

If need anymore information on this or our data I'd be happy to post it.

Thank you,

Hi Garrett-

Hmmm, what is the output of the following in the AP results directory:

abids_json_info.py -json out.ss_review_uvars.json -field vr_base_dset

And then, what is the output of:

3dBrickStat -slow -perclist 3 0 100 98 `abids_json_info.py -json out.ss_review_uvars.json -field vr_base_dset`



Hi Paul,

Here is the output for those two lines:

abids_json_info.py -json out.ss_review_uvars.json -field vr_base_dset

3dBrickStat -slow -perclist 3 0 100 98 `abids_json_info.py -json out.ss_review_uvars.json -field vr_base_dset`

** FATAL ERROR: -percentile can only be used on one sub-brick only.
Use sub-brick selectors '[.]' to specify sub-brick of interest.

This is with the selected sub-brick:

3dBrickStat -slow -perclist 3 0 100 98 `abids_json_info.py -json out.ss_review_uvars.json -field `[vr_base_external+orig.HEAD]``

usage: /Users/garrett/abin/abids_json_info.py [-json JSON [JSON ...]]
                                                    [-TR] [-TE] [-TE_sec]
                                                    [-field STR [STR ...]]
                                                    [-list_fields] [-help]
/Users/garrett/abin/abids_json_info.py: error: argument -field: expected at least one argument
3dBrickStat: No match.


Hi, Garrett-

The 3dBrickstat command being run here is actually this:

3dBrickStat -slow -perclist 3 0 100 98 vr_base_external+orig.HEAD

Ah, and I see that the issue is that this is a different dataset than the usual, auto-produced vr_base_min_outlier+orig.HEAD dset. You are using an external volume for reference, but you should ensure that this is just a single volume, not a multi-volume dataset. I suspect you are using the [0]th volume from it, but it would be better if you provided afni_proc.py just the [0]th volume in the first place. Then I think that this should be fine.


Hi Paul,

Here is the output for that with the 0th volume select:

3dBrickStat -slow -perclist 3 0 100 98 vr_base_external+orig.HEAD[0]
0.0 0.000000   100.0 883.031433   98.0 440.000000

I am currently rerunning it with having the external vr_base_dset with only the 0th volume select to be input into the afni_proc.py script. I will update you on it shortly.

Thank you,