Skip to content

Instantly share code, notes, and snippets.

View alexfoias's full-sized avatar

Alexandru Foias alexfoias

10 followers · 0 following
  • McGill
  • Montreal,Canada
View GitHub Profile
@alexfoias
alexfoias / openneuro
Created September 26, 2019 15:13
(base) alex-macbook:~ $ openneuro -V
3.6.0
(base) alex-macbook:~ $ npm -v
6.9.0
(base) alex-macbook:~ $ openneuro upload -i --dataset ds001919 /Volumes/sct_testing/bids/spineGeneric_multiSubjects
Adding files to "ds001919"
bids-validator@1.3.6
(node:6019) ExperimentalWarning: The fs.promises API is experimental
@alexfoias
alexfoias / error debian 8.11 - sct 4.2.1
Last active February 11, 2020 17:08
--
Spinal Cord Toolbox (4.2.1)
SCT info:
- version: 4.2.1
- path: /home/alex/sct_4.2.1
OS: linux (Linux-3.16.0-6-amd64-x86_64-with-debian-8.11)
CPU cores: Available: 4, Used by SCT: 4
RAM: MemTotal: 4058416 kB
total used free shared buffers cached
@alexfoias
alexfoias / error debian 8.11 - sct 4.0.0
Created February 11, 2020 17:09
--
Spinal Cord Toolbox (4.0.0)
SCT info:
- version: 4.0.0
- path: /home/alex/sct_4.0.0
OS: linux (Linux-3.16.0-6-amd64-x86_64-with-debian-8.11)
CPU cores: Available: 4, Used by SCT: 4
RAM: MemTotal: 4058416 kB
total used free shared buffers cached
@alexfoias
alexfoias / output console R
Last active February 12, 2020 16:56
Error deface T2w
> library(RNifti)
> library(fslr)
> getwd()
[1] "/Users/alfoi/Desktop/tst_r"
> setwd("/Users/alfoi/Desktop/tst_r")
> fname = "sub-chibaIngeniasub-chibaIngenia_T2w.nii.gz"
> download.file(url = paste0("https://openneuro.org/crn/datasets/ds002393/",
+ "snapshots/1.0.2/files/",
+ "sub-chibaIngenia:anat:sub-chibaIngenia_T2w.nii.gz"),
+ destfile = fname)
@alexfoias
alexfoias / output sct check dependencies from teamviewer
Last active March 2, 2020 17:03
test installation-failed-during-installation-of-keras
--
Spinal Cord Toolbox (git-master-d8d887c155dec9450da37a5ee4f02de3cf6cdca5)
SCT info:
- version: git-master-d8d887c155dec9450da37a5ee4f02de3cf6cdca5
- path: /home/alfoi_admin/dwld_sct/spinalcordtoolbox
OS: linux (Linux-4.15.0-88-generic-x86_64-with-debian-stretch-sid)
CPU cores: Available: 12, Used by SCT: 12
RAM: MemTotal: 65860608 kB
total used free shared buff/cache available
@alexfoias
alexfoias / upload error
Created March 11, 2020 17:28
(base) alex-macbook:~ $ openneuro upload -i --dataset ds001919 /Volumes/sct_testing/bids/spineGeneric_multiSubjects
Adding files to "ds001919"
bids-validator@1.4.3
Summary: Available Tasks: Available Modalities:
2485 Files, 7.89GB T1w
248 - Subjects T2star
1 - Session T2w
dwi
@alexfoias
alexfoias / gist:f50c72a0848bf9c176d0c230b93d43ab
Created March 30, 2020 18:53
datalad install problem ds002393
datalad install -g https://github.com/OpenNeuroDatasets/ds002393.git
[INFO ] Detected a filesystem without fifo support.
[INFO ] Disabling ssh connection caching.
[INFO ] Detected a crippled filesystem.
[INFO ] Entering an adjusted branch where files are unlocked as this filesystem does not support locked files.
Checking out files: 100% (130/130), done. )
[INFO ] Switched to branch 'adjusted/master(unlocked)'
[INFO ] Remote origin not usable by git-annex; setting annex-ignore
install(ok): /home/alfoi/duke/temp/alfoi/test/ds002393 (dataset)
Total (0 ok, 130 failed out of 130): 0%| | 0.00/810M [00:01<?, ?B/s][WARNING] Running get resulted in stderr output: git-annex: get: 130 failed
@alexfoias
alexfoias / gist:255a4ff4c8a690333f45555de9c437ae
Created May 6, 2020 18:21
datalad status output
This file has been truncated, but you can view the full file.
untracked: .datalad (directory)
modified: .gitattributes (file)
modified: CHANGES.md (file)
modified: README.txt (file)
modified: dataset_description.json (file)
untracked: derivatives (directory)
modified: participants.json (file)
modified: participants.tsv (file)
untracked: sub-amuAMU15001 (directory)
untracked: sub-amuAMU15002 (directory)
@alexfoias
alexfoias / Pytest
Last active November 5, 2020 15:35
pytest on 2193729161ef1b90d76eb2c4554eea4414532a34
[5/11/20 10:31:11] (base) alex@NeuroPoly-MacBook-Pro shimming-toolbox % git rev-parse origin/master
2193729161ef1b90d76eb2c4554eea4414532a34
[5/11/20 10:29:24] (base) alex@NeuroPoly-MacBook-Pro shimming-toolbox % pytest
INFO:root:/Users/alex/code/shimming-toolbox/testing_data, testing_data
INFO:shimmingtoolbox.download:Trying URL: https://github.com/shimming-toolbox/data-testing/archive/r20201021.zip
INFO:shimmingtoolbox.download:Downloading: data-testing-r20201021.zip
Status: 11.4MB [00:02, 4.85MB/s]
INFO:shimmingtoolbox.download:Unzip data to: /var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/st_download_a37h4cm7
INFO:shimmingtoolbox.download:Removing temporary folders...
@alexfoias
alexfoias / pytest without prelude or dcm2niix
Created November 5, 2020 19:12
pytest without prelude or dcm2niix
[5/11/20 2:10:05] (base) alex@NeuroPoly-MacBook-Pro shimming-toolbox % pytest -m "not prelude and not dcm2niix"
INFO:root:/Users/alex/code/shimming-toolbox/testing_data, testing_data
INFO:shimmingtoolbox.download:Trying URL: https://github.com/shimming-toolbox/data-testing/archive/r20201021.zip
INFO:shimmingtoolbox.download:Downloading: data-testing-r20201021.zip
Status: 100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 11.4M/11.4M [00:00<00:00, 13.9MB/s]
INFO:shimmingtoolbox.download:Unzip data to: /var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/st_download_8k3rb4g3
INFO:shimmingtoolbox.download:Removing temporary folders...
============================================================================================== test session starts ===============================================================================================
platform darwin -- Python 3.8.3, pytest-4.6.11, py-1.9.0, plu