SSWarper not running to completion

AFNI Message Board
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AFNI version info (afni -ver): 21.3.04

Hi. We are having a hard time figuring out why SSWarper is not running to completion for one particular participant. The script successfully produced the anatUAC, anatUA, anatU, and anatS, but did not produce the anatQQ file or any others. Below is the script for running SSWarper as well as the Init file output. Could you please help us figure out how we should proceed? Thank you!

![image|564x500](upload://gHjFWkslIIUSGMOaJr1HszqXi3R.jpeg)
![SSWarper_975Init|690x397](upload://1kGoGTIeqZHc1SvjzI1MZReLKzc.png)
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SSWarper_975Init
SSWarper_975Init944×544 191 KB

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image
image1029×912 126 KB

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Hi-

That is a pretty old version of AFNI, now about two years old. I would likely update it, for starters.

Could you please paste the output of the terminal text? That would help point out where there is a problem.

The first thing I would check for would be the initial overlap between the anatomical and the template. If they are very far apart, badness might happen in alignment and/or grid generation.

@djunct_overlap_check                                    \
   -ulay __T1_mpr_ns_sag_ADNI_176mm_20230919104852_2.nii \
   -olay ~/REF_TEMPLATES/MNI152_2009_template_SSW.nii.gz

Image(s) made by this function should actually be produced in your output @SSwarper directory, as described in the help here:

  init_qc_00_overlap_uinp_obase.jpg
    o [ulay] original source dset
      [olay] original base dset
    o single image montage to check initial overlap of source and base,
      ignoring any obliquity that might be present (i.e., the way AFNI 
      GUI does by default, and also how alignment starts)
    o if initial overlap is not strong, alignment can fail or
      produce weirdness
    o *if* either dset has obliquity, then an image of both after 
      deobliquing with 3dWarp is created (*DEOB.jpg), and a text file
      about obliquity is also created (*DEOB.txt).

Could you please run that above command and post the image(s) here, too?

--pt