[BUG] bidsCopyInputFolder doesn't follow output directory

[JacMatu]

Is there an existing issue for this?

• I have searched the existing issues

Operating system

• Linux
• Mac
• Windows

Operating system version

No response

SPM 12 version

• 7771
• 7487
• 7219

Platform

• MATLAB
• Octave

Platform version

• MATLAB 2019a
• Octave 4.2.2

bidspm version

v3.1.0

bidspm branch / commit number

No response

Expected Behavior

I'm running
bidsCopyInputFolder(opt,'unzip', true)
with intention to copy and unzip data from raw to derivatives/bidspm-preproc for further processing (generating T1 maps)

dirs are set up like this:
opt.dir.input = fullfile(root_dir, 'inputs', 'raw'); opt.dir.derivatives= fullfile(root_dir,'outputs','derivatives'); opt.dir.output = fullfile(root_dir,'outputs','derivatives', 'bidspm-preproc');

with my expectancy to copy and unzip stuffs from opt.dir.input to opt.dir.output, e.g. to have an unzipped files in derivatives/bidspm-preproc

BIDS stats model

No response

Current Behavior & Error message

Instead, bidsCopyInputFolder creates a new dir in derivatives, called simply bidspm, ignoring my target output to store unzipped data.

Anything else?

can it be caused by

    bids.copy_to_derivative(BIDS, ...
                            'pipeline_name', pipeline_name, ...
                            'out_path', fullfile(opt.dir.output, '..'), ...
                            'filter', filter, ...
                            'unzip', unzip, ...
                            'force', force, ...
                            'skip_dep', skip_dependencies, ...
                            'use_schema', use_schema, ...
                            'verbose', opt.verbosity > 0, ...
                            'tolerant', TOLERANT);

I see 'out_path', fullfile(opt.dir.output, '..') to skip one dir above the output.
When I changed it to 'out_path', opt.dir.output files were copied and unzipped to `derivatives/bidspm-preproc/bidspm'

This never happened when I used bidspm workflows like preproc (that also include copying and unzipping data), just when I want to use that function in isolation to prepare for things that are not covered by main workflows (T1 map generation, data upsampling, denoising with presurfer, etc.)

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