This collection contains a recipe to start a girder instance with a public IP by combining Vagrant with docker.
Satrajit Ghosh satra
satra
/ README.md
Last active
June 4, 2016 23:58
Vagrant + docker + nginx + girder (https://github.com/girder/girder/issues/1358)
satra
/ test.ipynb
Created
April 28, 2016 18:12
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| { | |
| "name": "grep", | |
| "tool-version": "2.21", | |
| "description": "Linux grep tool.", | |
| "command-line": "grep [IGNORE_CASE] [MAX_COUNT] [PATTERN] [FILE] > [STDOUT]", | |
| "docker-image": "ubuntu", | |
| "docker-index": "http://index.docker.io", | |
| "schema-version": "0.2", | |
| "inputs": [ | |
| { |
satra
/ image_mask.py
Last active
August 29, 2015 14:14
QQA: compute the volume of contrasts and sort them by size
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| from glob import glob | |
| import os | |
| import numpy as np | |
| fl = glob('model01/task001/SAD_???/copes/mni/model001/task001_cope01.nii.gz') | |
| os.system('fslmerge -t output.nii.gz %s' % ' '.join(fl)) | |
| os.system('fslmaths output.nii.gz -abs -thr 1 -bin output2') | |
| os.system('fslstats -t output2 -V > output2.txt') | |
| foo = np.genfromtxt('output2.txt') | |
| idx = np.argsort(foo[:, 1]) | |
| zip(np.array(fl)[idx], foo[idx, 1]) |
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| #!/bin/bash | |
| for sub in '315' '318' '332' ; do | |
| for run in 1 2 3 4 ; do | |
| mkdir /om/project/gates/wmfilt/openfmri/ds001/${sub} | |
| mkdir /om/project/gates/wmfilt/openfmri/ds001/${sub}/model | |
| mkdir /om/project/gates/wmfilt/openfmri/ds001/${sub}/model/model001 | |
| mkdir /om/project/gates/wmfilt/openfmri/ds001/${sub}/model/model001/onsets | |
| mkdir /om/project/gates/wmfilt/openfmri/ds001/${sub}/model/model001/onsets/task001_run00${run} | |
| mkdir /om/project/gates/wmfilt/openfmri/ds001/${sub}/BOLD |
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| <!DOCTYPE html> | |
| <html lang="en"> | |
| <head> | |
| <meta charset="utf-8"> | |
| <title>Photo Viewer for Local Files and Directories</title> | |
| <meta name="viewport" content="width=device-width, initial-scale=1.0"> | |
| <link rel="stylesheet" href="http://static.jstree.com/3.0.4/assets/dist/themes/default/style.min.css" /> | |
| <link rel="stylesheet" type="text/css" href="http://rii.uthscsa.edu/mango/papaya/papaya.css?version=0.6.5&build=692" /> | |
| <script type="text/javascript" src="http://rii.uthscsa.edu/mango/papaya/papaya.js?version=0.6.5&build=692"></script> |
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| from scipy.spatial.distance import pdist, squareform | |
| import numpy as np | |
| from numbapro import jit, float32 | |
| def distcorr(X, Y): | |
| """ Compute the distance correlation function | |
| >>> a = [1,2,3,4,5] | |
| >>> b = np.array([1,2,9,4,4]) |
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| from nipype import Workflow, Node, Function | |
| def myrandomfunc(N): | |
| import numpy as np | |
| return np.random.random_integers(1, 10, N) | |
| def mysumfunc(X): | |
| return X.sum() | |
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| $ find SUB_1024011/resting -type f | |
| SUB_1024011/resting/mask_files/median_brain_mask.nii | |
| SUB_1024011/resting/mask_files/T1_out_brain_pve_0_maths_warped.nii | |
| SUB_1024011/resting/mask_files/T1_out_brain_pve_1_maths_warped.nii | |
| SUB_1024011/resting/mask_files/T1_out_brain_pve_2_maths_warped.nii | |
| SUB_1024011/resting/mask_files/target/output_warped_image_maths.nii | |
| SUB_1024011/resting/parcellations/aparc/smooth/rest_01_avgwf.txt | |
| SUB_1024011/resting/parcellations/aparc/smooth/rest_01_summary.stats | |
| SUB_1024011/resting/parcellations/aparc/smooth/rest_02_avgwf.txt | |
| SUB_1024011/resting/parcellations/aparc/smooth/rest_02_summary.stats |
satra
/ tracula.py
Created
September 23, 2014 22:38
Diffusion processing with bedpostx_gpu, tracula and dipy
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| import os | |
| from glob import glob | |
| from nipype import config | |
| config.enable_provenance() | |
| from nipype import Node, Function, Workflow, IdentityInterface | |
| from nipype.interfaces.io import SelectFiles, DataSink | |
| import os |