[BUG] gunzip input images is not done (cat12 can do it internally)

[FeHoff]

What version of the bids app were you using?

testing cat12:unstable docker

Describe your problem in detail.

input data is not found

2024-10-01 08:48:11,503 [    INFO] indexing /ds000001
2024-10-01 08:48:13,029 [    INFO] processing subjects: ['01']
copying subjects ⠋ 0:00:00 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 0/1   0% -:--:--2024-10-01 08:48:13,032 [    INFO] Copying 03
2024-10-01 08:48:13,040 [    INFO] Copying /ds000001/sub-03/anat/sub-03_T1w.nii.gz to /ds000001/derivatives/CAT12_0.1.dev8+gc517f60
copying subjects   0:00:00 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1/1 100% 0:00:00
2024-10-01 08:48:13,316 \[    INFO\] indexing /ds000001/derivatives/CAT12\_0.1.dev8+gc517f60
2024-10-01 08:48:13,406 \[    INFO\] segment\_type='default' - using batch cat\_standalone\_segment.m.
processing subjects ⠋ 0:00:00 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 0/1   0% -:--:--2024-10-01 08:48:13,419 \[ WARNING\] No data found for subject 01.
processing subjects ⠋ 0:00:00 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 0/1   0% -:--:--

it's at the right folder but still zipped:
ds000001/derivatives/CAT12_0.1.dev8+gc517f60
├── [ 618]  dataset_description.json
├── [4.0K]  logs
│   ├── [9.7K]  cat_standalone_segment.m
│   └── [ 169]  CITATION.md
├── [4.0K]  sub-01
    └── [4.0K]  anat
        └── [5.5M]  sub-01_T1w.nii.gz

when doing gunzip manually outside the app, the same command works:

2024-10-01 09:12:38,672 [    INFO] indexing /ds000001
2024-10-01 09:12:40,292 [    INFO] processing subjects: ['01']
copying subjects ⠋ 0:00:00 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 0/1   0% -:--:--2024-10-01 09:12:40,295 [    INFO] Copying 01
2024-10-01 09:12:40,307 [    INFO] Copying /ds000001/sub-01/anat/sub-01_T1w.nii.gz to /ds000001/derivatives/CAT12_0.1.dev8+gc517f60
copying subjects   0:00:00 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1/1 100% 0:00:00
2024-10-01 09:12:40,606 [    INFO] indexing /ds000001/derivatives/CAT12_0.1.dev8+gc517f60
2024-10-01 09:12:40,701 [    INFO] segment_type='default' - using batch cat_standalone_segment.m.
processing subjects ⠋ 0:00:00 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 0/1   0% -:--:--2024-10-01 09:12:40,716 [    INFO] ['/opt/CAT12.8.1_r2042_R2017b/standalone/cat_standalone.sh', '/ds000001/derivatives/CAT12_0.1.dev8+gc517f60/sub-01/anat/sub-01_T1w.nii', '-b', 'cat_standalone_segment.m']
------------------------------------------
Setting up environment variables
---
LD_LIBRARY_PATH is .:/opt/MCR-2017b/v93/runtime/glnxa64:/opt/MCR-2017b/v93/bin/glnxa64:/opt/MCR-2017b/v93/sys/os/glnxa64:/opt/MCR-2017b/v93/sys/opengl/lib/glnxa64
SPM12, version 7771 (standalone)
MATLAB, version 9.3.0.713579 (R2017b)
 ___  ____  __  __                                            
/ __)(  _ \(  \/  )                                           
\__ \ )___/ )    (   Statistical Parametric Mapping           
(___/(__)  (_/\/\_)  SPM12 - https://www.fil.ion.ucl.ac.uk/spm/

Item 'Grey Matter', field 'val': No matching defaults value found.
Item 'White Matter', field 'val': No matching defaults value found.
Item 'Cerebro-Spinal Fluid', field 'val': No matching defaults value found.
Item 'Bias Corrected', field 'val': No matching defaults value found.
Item 'Clean up any partitions', field 'val': No matching defaults value found.
Item 'Tissue probability maps', field 'val': No matching defaults value found.
Item 'Gaussians per class', field 'val': No matching defaults value found.
Item 'Affine Regularisation', field 'val': No matching defaults value found.
Item 'Warping Regularisation', field 'val': No matching defaults value found.
Item 'Warp Frequency Cutoff', field 'val': No matching defaults value found.
Item 'Bias regularisation', field 'val': No matching defaults value found.
Item 'Bias FWHM', field 'val': No matching defaults value found.
Item 'Sampling distance', field 'val': No matching defaults value found.


------------------------------------------------------------------------
01-Oct-2024 09:12:53 - Running job #1
------------------------------------------------------------------------
01-Oct-2024 09:12:54 - Running 'CAT12: Segmentation'

------------------------------------------------------------------------
CAT12.8.1 r2040: 1/1:                         ./sub-01/anat/sub-01_T1w.n
------------------------------------------------------------------------
SANLM denoising (medium):                                            27s
Internal resampling (1.00x1.33x1.33mm > 1.00x1.00x1.00mm):            1s
APP: Rough bias correction:                                       
  Initialize                                                          7s

What command did you run?

docker run --rm -ti -v "$(pwd)"/ds000001:/ds000001 bids/cat12:unstable /ds000001 /ds000001/derivatives participant segment --participant_label 01

Describe what you expected.

cat12 standalone doing its thing