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edickie / ciftify

The tools of the Human Connectome Project (HCP) adapted for working with non-HCP datasets
https://edickie.github.io/ciftify/
MIT License
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trouble running the example subjects #131

Closed renxili closed 4 years ago

renxili commented 4 years ago

Hi, I have install the citify via both the manually prepared environment and Docker, and was trying to go through the example subjects. I have run into these errors when trying to convert the free surfer output to HCP output:

ciftify_recon_all --ciftify-work-dir Users/renxili/Desktop/PINT_test/ciftify_demo_01 --fs-subjects-dir /Users/renxili/Desktop/PINT_test/ds000030_R1.0.4/derivatives/freesurfer sub-50005 /Users/renxili/opt/anaconda3/lib/python3.7/site-packages/ciftify/utils.py:286: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details. config = yaml.load(yaml_stream) Traceback (most recent call last): File "/Users/renxili/opt/anaconda3/bin/ciftify_recon_all", line 11, in load_entry_point('ciftify==2.0.3', 'console_scripts', 'ciftify_recon_all')() File "/Users/renxili/opt/anaconda3/lib/python3.7/site-packages/ciftify/bin/ciftify_recon_all.py", line 1422, in main settings = Settings(arguments) File "/Users/renxili/opt/anaconda3/lib/python3.7/site-packages/ciftify/bin/ciftify_recon_all.py", line 192, in init self.reg_name = self.set_registration_mode(arguments) File "/Users/renxili/opt/anaconda3/lib/python3.7/site-packages/ciftify/bin/ciftify_recon_all.py", line 209, in set_registration_mode verify_msm_available() File "/Users/renxili/opt/anaconda3/lib/python3.7/site-packages/ciftify/bin/ciftify_recon_all.py", line 369, in verify_msm_available msm = ciftify.config.find_msm() File "/Users/renxili/opt/anaconda3/lib/python3.7/site-packages/ciftify/config.py", line 68, in find_msm return msm.replace(os.linesep, '') AttributeError: 'NoneType' object has no attribute 'replace'

I have already update the YAML to 5.3.1 and my python is on 3.8.2 running on a Mac OS. Do you have any ideas on how I should solve these error? Thanks so much!