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nipreps / mriqc

Automated Quality Control and visual reports for Quality Assessment of structural (T1w, T2w) and functional MRI of the brain
http://mriqc.readthedocs.io
Apache License 2.0
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Trait Error after installing SynthStrip #1252

Closed madeleinebarter closed 7 months ago

madeleinebarter commented 7 months ago

What happened?

I installed the newest versions of FSL and Freesurfer, and also installed SynthStrip using the install instructions, but I am still receiving the error: traits.trait_errors.TraitError: The 'model' trait of a _SynthStripInputSpec instance must be a pathlike object or string representing an existing file, but a value of '' <class 'str'> was specified.

What command did you use?

mriqc bids mriqc_folder participant --participant-label sub-001

What version of the software are you running?

23.1.1

How are you running this software?

Local installation ("bare-metal")

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

No response

Additional information / screenshots

No response

oesteban commented 7 months ago

Can you provide execute this in the same shell you were running mriqc?

echo $FREESURFER_HOME
oesteban commented 7 months ago

Thanks for reporting - I've added all necessary details here https://mriqc--1254.org.readthedocs.build/en/1254/install.html#execution-system-dependencies and improve the feedback to the user.

Please reopen if this remains a problem after the documentation update.