T1w images incorrectly detected as skull-stripped (difference between 0.12.2 -> 0.13.1)

[psadil]

Describe the bug

I have T1w images like the following that are being detected as having had their skulls already stripped

With 0.12.2, the skulls were detected as needing to be stripped.

Exact command line executed

$ singularity build smriprep_0.13.1.sif docker://nipreps/smriprep:0.13.1
$ singularity run -e --bind ${root}:/ds --bind ${scratch}:/scratch code/smriprep_0.13.1.sif --nprocs 16 --omp-nthreads 8 --mem-gb 24 --output-spaces T1w MNI152NLin2009cAsym MNI152NLin6Asym --fs-license-file /ds/smriprep/code/license -w /scratch/work --participant-label AAO1062 --no-submm-recon /ds/bids/rawdata /ds/smriprep/derivatives participant

Are you positive that the input dataset is BIDS-compliant?

• I have used the online BIDS-Validator
• I have run a local installation of the BIDS-Validator (please, note the version of the validator here).
• I let sMRIPrep check it for me (in other words, I didn't set the --skip-bids-validation argument).
• No, I haven't checked myself AND used the --skip-bids-validation argument.

sMRIPrep feedback information
Please attach the full log written to the standard output and the crashfile(s), if generated.

231128-18:11:30,567 nipype.workflow Level 25:
	 
    Running sMRIPrep version 0.13.1:
      * BIDS dataset path: /ds/bids/rawdata.
      * Participant list: ['AAO1062'].
      * Run identifier: 20231128-181104_1efc0d9c-4437-4a93-8ebe-27a4f3bd9a0e.

    Spatial References: T1w, MNI152NLin2009cAsym:res-native, MNI152NLin6Asym:res-native
    
231128-18:11:31,929 nipype.workflow INFO:
	 ANAT Stage 1: Adding template workflow
231128-18:11:34,226 nipype.workflow INFO:
	 ANAT Stage 2: Preparing brain extraction workflow
231128-18:11:35,37 nipype.workflow INFO:
	 ANAT Stage 2: Skipping skull-strip, INU-correction only
231128-18:11:35,59 nipype.workflow INFO:

full log (note that this run crashed due to what I believe to be an unrelated reason)

Visual reports of sMRIPrep
If applicable, add screenshots or attach the corresponding "reportlets" to help explain your problem.

Installation type (please complete the following information):

• "Bare-metal"
• Singularity
• Docker

Additional context
Add any other context about the problem here.

smriprep/smriprep/workflows/anatomical.py

Line 798 in e460f6d

run_skull_strip = all(_is_skull_stripped(img) for img in t1w)

ends up evaluating to False

[effigies]

TBH I thought this check was so bad nobody used it, but it turns out it's default on smriprep.

Looks like it should be run_skull_strip = not all(...). Thanks for catching this. Care to open a PR?