Tips for using anonymiser option about dcm2bids HOT 7 CLOSED

Pydeface can be called as a script, so that should work. When you pip install it you will end up with a 'pydeface' CLI.

Let me know if that works - I originally developed the anonymiser feature to work with pydeface, but it looks like they may have refactored the code a bit since last time I used it.

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Another option is quickshear.

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I tried with pydeface, both directly put as an option in dcm2bids call, and wrapped in a following simple script:

#!/bin/bash
pydeface --outfile $2 --verbose $1

I also made sure its executable. I get an error, that the output file from the subprocess call cannot be found and dcm2bids stops execution.

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You shouldn't need a shell script wrapper. Pydeface is a command line application. Try putting in the absolute path to pydeface instead of just the name. It might not be on path in the session you're running python in.

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Ok, it was a path issue, of different sort, thanks for the help.

Though, supply pydeface directly as an argument -a /home/hstojic/.pyenv/nipy/bin/pydeface does not work. I get the following error:

INFO:dcm2bids:subprocess:  /home/hstojic/.pyenv/nipy/bin/pydeface /media/hstojic/dataneuro/fnclearning_fmri/dBids/tmp_dcm2bids/sub-s087/002_20190128.MQ05073_FIL_MPRAGE_64ch_Head_20190128184304.nii.gz /media/hstojic/dataneuro/fnclearning_fmri/dBids/sub-s087/anat/sub-s087_T1w.nii.gz
INFO:dcm2bids:
usage: pydeface [-h] [--outfile path] [--force] [--applyto  [...]]
                [--cost mutualinfo] [--template path] [--facemask path]
                [--nocleanup] [--verbose]
                path
pydeface: error: unrecognized arguments: /media/hstojic/dataneuro/fnclearning_fmri/dBids/sub-s087/anat/sub-s087_T1w.nii.gz
------------
pydeface 2.0
------------

I think this is because new version of pydeface accepts a single argument, additional flags are needed for output file. Wrapping it in a shell script as in my previous comment works.

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Ah, got it. Thanks for looking into this.

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Thanks for reporting this.
It's now possible to add the option defaceTpl in the configuration file.

For this version of pydeface : "defaceTpl": "pydeface -outfile {dstFile} {srcFile}"

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