Yaml file

[APaulk]

Hello, I am finding something odd and I cannot figure out why it is erroring out. It's likely something I am entering incorrectly.

On Ubuntu 20, did the following install for ciftify: $ pip install https://github.com/edickie/ciftify/archive/2.0.3-beta.tar.gz And installed FSL 6.0.5.2 And entered the test "ciftify_vol_result --help" and the output indicates ciftify was installed correctly.

When we enter: $ ciftify_recon_all --ciftify-work-dir /home/cashlab/Documents/Recons/ciftifyTest --fs-subjects-dir /home/cashlab/Documents/tools/freesurfer/subjects sub-0t3i_SurferOutput

We get the following output: Cannot read yaml config file /home/cashlab/.pyenv/versions/3.7.7/lib/python3.7/site-packages/ciftify/data/ciftify_workflow_settings.yaml, check formatting.

I went a yaml parser check (https://yaml-online-parser.appspot.com/ ) and the file is fine. Has anyone else run into this issue? Thank you, Angelique Paulk

[DESm1th]

Hi Angelique!

You may have already solved this issue yourself, but this is because you're using an older version of ciftify that contains a bug in how it reads yaml files.

The simplest solution is to install a newer version (just pip install ciftify). But if you need your current version of ciftify for some reason open /home/cashlab/.pyenv/versions/3.7.7/lib/python3.7/site-packages/ciftify/utils.py and in the __read_settings function find the line that looks like this: config = yaml.load(yaml_stream) and change it to config = yaml.load(yaml_stream, Loader=yaml.SafeLoader)

[APaulk]

Hi, Thank you for getting back to me! This helps. I had actually installed the most recent ciftify with that command you list but the fix you suggested is great. Unless you mean an updated python version? Thank you, Angelique

[DESm1th]

The version you're installing with that command is 2.0.3. If you use plain old pip install ciftify it will install 2.3.3 which has a fix for that bug (and other bugs you may run into)