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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
116 stars 157 forks source link

bug in 2.0.3 #66

Closed oricon closed 6 years ago

oricon commented 6 years ago

I think there might be a bug in the latest update. I tried installed the update with pip but there was an error. (I replicated the problem on another computer with Python 3.6.5)

Successfully built ciftify Installing collected packages: ciftify Exception: Traceback (most recent call last): File "/apps/psyc/anaconda3/python35_520/lib/python3.6/site-packages/pip/_internal/basecommand.py", line 228, in main status = self.run(options, args) File "/apps/psyc/anaconda3/python35_520/lib/python3.6/site-packages/pip/_internal/commands/install.py", line 335, in run use_user_site=options.use_user_site, File "/apps/psyc/anaconda3/python35_520/lib/python3.6/site-packages/pip/_internal/req/init.py", line 49, in install_given_reqs **kwargs File "/apps/psyc/anaconda3/python35_520/lib/python3.6/site-packages/pip/_internal/req/req_install.py", line 748, in install use_user_site=use_user_site, pycompile=pycompile, File "/apps/psyc/anaconda3/python35_520/lib/python3.6/site-packages/pip/_internal/req/req_install.py", line 961, in move_wheel_files warn_script_location=warn_script_location, File "/apps/psyc/anaconda3/python35_520/lib/python3.6/site-packages/pip/_internal/wheel.py", line 327, in move_wheel_files console, gui = get_entrypoints(ep_file) File "/apps/psyc/anaconda3/python35_520/lib/python3.6/site-packages/pip/_internal/wheel.py", line 143, in get_entrypoints console = dict(_split_ep(v) for v in console.values()) ValueError: dictionary update sequence element #4 has length 3; 2 is required

So I did a manual install and still have an issue running commands:

[joseph.orr@gfx bin$ ciftify_subject_fmri --SmoothingFWHM 2 --ciftify-work-dir $outdir --already-in-MNI $func $subject $label Fatal Python error: Py_Initialize: can't initialize sys standard streams Traceback (most recent call last): File "/apps/psyc/ciftify/2.0.3/ciftify/io.py", line 9, in File "/apps/psyc/anaconda3/python35_520/lib/python3.6/logging/init.py", line 26, in File "/apps/psyc/anaconda3/python35_520/lib/python3.6/traceback.py", line 5, in File "/apps/psyc/anaconda3/python35_520/lib/python3.6/linecache.py", line 11, in File "/apps/psyc/anaconda3/python35_520/lib/python3.6/tokenize.py", line 27, in ImportError: cannot import name 'open' Aborted (core dumped)

edickie commented 6 years ago

Thanks for lettinge know. Will debug today.

edickie commented 6 years ago

We think we fixed everything with the 2.0.4-alpha version.

oricon commented 6 years ago

Hi the install works without a problem, but now I run into an error with niio in ciftify_subject_fmri when it gets to the Subcortical Processing:

Traceback (most recent call last): File "/apps/psyc/ciftify/2.0.4/ciftify/bin/ciftify_subject_fmri", line 1062, in main() File "/apps/psyc/ciftify/2.0.4/ciftify/bin/ciftify_subject_fmri", line 1057, in main ret = run_ciftify_subject_fmri(settings, tmpdir) File "/apps/psyc/ciftify/2.0.4/ciftify/bin/ciftify_subject_fmri", line 190, in run_ciftify_subject_fmri tmpdir) File "/apps/psyc/ciftify/2.0.4/ciftify/bin/ciftify_subject_fmri", line 893, in subcortical_atlas func_vx_size = ciftify.niio.voxel_spacing(input_fMRI) AttributeError: module 'ciftify' has no attribute 'niio'

Here's the last line of the ciftify_subject_fmri.log:

2018-06-23 15:53:57.789319 : Subcortical Processing

VolumefMRI: /fdata/scratch/joseph.orr/adaptcog/fmri/hcp/sub-M80301092/MNINonLinear/Results/task-ritl_acq-MB_run-01/task-ritl_acq-MB_run-01.nii.gz

edickie commented 6 years ago

oops sorry. It looks like the final bug fixes were not included in the 2.0.4 release. 2.0.5 has been pushed.

On Sat, Jun 23, 2018 at 5:09 PM, Joseph M. Orr notifications@github.com wrote:

Hi the install works without a problem, but now I run into an error with niio in ciftify_subject_fmri when it gets to the Subcortical Processing:

Traceback (most recent call last): File "/apps/psyc/ciftify/2.0.4/ciftify/bin/ciftify_subject_fmri", line 1062, in main() File "/apps/psyc/ciftify/2.0.4/ciftify/bin/ciftify_subject_fmri", line 1057, in main ret = run_ciftify_subject_fmri(settings, tmpdir) File "/apps/psyc/ciftify/2.0.4/ciftify/bin/ciftify_subject_fmri", line 190, in run_ciftify_subject_fmri tmpdir) File "/apps/psyc/ciftify/2.0.4/ciftify/bin/ciftify_subject_fmri", line 893, in subcortical_atlas func_vx_size = ciftify.niio.voxel_spacing(input_fMRI) AttributeError: module 'ciftify' has no attribute 'niio' Here's the last line of the ciftify_subject_fmri.log: 2018-06-23 15:53:57.789319 : Subcortical Processing

VolumefMRI: /fdata/scratch/joseph.orr/adaptcog/fmri/hcp/sub- M80301092/MNINonLinear/Results/task-ritl_acq-MB_run- 01/task-ritl_acq-MB_run-01.nii.gz

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oricon commented 6 years ago

Looks like this bug is fixed, thanks!