Agah agahkarakuzu
🏠
agahkarakuzu
/ gist:97dbc6f89652576d4b1de1d01b8a8669
Created
June 17, 2025 15:19
Neuromosaics paper.md frontmatter
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| --- | |
| title: 'NeuroMOSAICS: A collection of neurostimulation datasets - Multi-scale Open-Source Across Interfaces Conditions & Species.' | |
| tags: | |
| - Neurostimulation | |
| - Optimization | |
| - Machine learning | |
| - Open source dataset | |
| authors: | |
| - name: Lison Kardassevitch | |
| affiliation: "1,2,3" |
agahkarakuzu
/ nextflow_agah.config
Created
July 22, 2022 13:46
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| process { | |
| withName: alignMtsatInputs { | |
| cpus = 1 | |
| memory = 0.5.GB | |
| maxForks = 5 | |
| container = 'qmrlab/antsfsl:latest' | |
| } | |
| withName: publishOutputs { | |
| cpus = 1 | |
| memory = 1.GB |
agahkarakuzu
/ neuromod-stat-anat-new.nf
Created
July 22, 2022 13:41
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| nextflow.enable.dsl=2 | |
| include { getSubSesEntity; checkSesFolders } from './modules/bids_patterns' | |
| params.bids = false | |
| params.help = false | |
| if (params.platform == "octave"){ | |
| if (params.octave_path){ | |
| log.info "Using Octave executable declared in nextflow.config." |
agahkarakuzu
/ lsline_octaeve.m
Created
June 10, 2020 07:41
MATLAB's `lsline` function, super simple Octave version.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| function [xl,y_bfl] = lsline_octave(X,Y,axsh) | |
| xl = get(axsh,'xlim'); | |
| yl = get(axsh,'ylim'); | |
| pf = polyfit(X,Y,1); | |
| y_bfl = pf(1)*xl + pf(2); | |
| hold on; | |
| plot(xl,y_bfl,'r','LineWidth',4); | |
| set(axsh,'xlim',xl); | |
| set(axsh,'ylim',yl); |
agahkarakuzu
/ environment.yml
Created
May 23, 2020 13:34
Conda environment for RRSG2020 (Exported from OSX)
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: sos_matlab | |
| channels: | |
| - defaults | |
| dependencies: | |
| - appnope=0.1.0=py36hf537a9a_0 | |
| - backcall=0.1.0=py36_0 | |
| - ca-certificates=2020.1.1=0 | |
| - certifi=2020.4.5.1=py36_0 | |
| - decorator=4.4.2=py_0 | |
| - ipython=7.2.0=py36h39e3cac_0 |
agahkarakuzu
/ gist:7dcfb7d0abd4c27d88ce6163901d2f42
Created
January 21, 2020 14:11
Elastix build exception
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| In file included from /home/jovyan/work/build/Elastix/Common/CostFunctions/itkAdvancedImageToImageMetric.h:28:0, | |
| from /home/jovyan/work/build/Elastix/Common/itkMultiResolutionImageRegistrationMethod2.h:43, | |
| from /home/jovyan/work/build/Elastix/Core/ComponentBaseClasses/elxRegistrationBase.h:25, | |
| from /home/jovyan/work/build/Elastix/Core/Kernel/elxElastixTemplate.h:30, | |
| from /home/jovyan/work/build/Elastix/Core/Install/elxIncludes.h:39, | |
| from /home/jovyan/work/build/Elastix/Components/FixedImagePyramids/FixedRecursivePyramid/elxFixedRecursivePyramid.h:21, | |
| from /home/jovyan/work/build/Elastix/Components/FixedImagePyramids/FixedRecursivePyramid/elxFixedRecursivePyramid.cxx:19: | |
| /home/jovyan/work/build/Elastix/Common/CostFunctions/itkLimiterFunctionBase.h:102:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] | |
| virtual void Initialize( void ) throw ( ExceptionObject ) {} | |
agahkarakuzu
/ gist:8d7a96cafb53ac823974ff4dcbc896a9
Created
June 2, 2017 00:53
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 0 info it worked if it ends with ok | |
| 1 verbose cli [ '/usr/bin/nodejs', | |
| 1 verbose cli '/usr/bin/npm', | |
| 1 verbose cli 'install', | |
| 1 verbose cli 'sodium', | |
| 1 verbose cli '--unsafe-perm' ] | |
| 2 info using npm@3.5.2 | |
| 3 info using node@v4.2.6 | |
| 4 verbose config Skipping project config: /home/agah/.npmrc. (matches userconfig) | |
| 5 silly loadCurrentTree Starting |