margulies’s gists

margulies / x.discord_backup.sh

Created February 14, 2023 11:14

Shell script for backing up discord server

	#!/bin/bash

	# Install DiscordChatExporter.Cli from:
	# https://github.com/Tyrrrz/DiscordChatExporter
	#
	# .NET runtime also needs to be installed:
	# https://github.com/Tyrrrz/DiscordChatExporter/blob/master/.docs/Dotnet.md
	#
	# Find your token and server ID ('guild'):
	# https://github.com/Tyrrrz/DiscordChatExporter/blob/master/.docs/Token-and-IDs.md

margulies / x.calc_gradient_extrema_zones.sh

Created March 26, 2021 16:31

To calculate the DMN nodes on the individual level based on the principal gradient

	#!/bin/bash

	# set global variables:
	subject_list = "XXXXX1 XXXXX2 XXXXX3 XXXXX4"
	comp = 0 # for the first component
	dir = "/XXXX/XXX" # location of data

	zone_rois = "....

	# find local extrema within each zone for each individual

margulies / steps_vted.sh

Created April 22, 2020 12:47

	# run the following conversion for each individual left and right hemisphere matrix separately

	# convert matrices to nifti1:
	wb_command -cifti-convert -to-nifti input.dconn.nii output.nii

	# convert matrices to vista:
	# after install lipsia:
	export dir=[directory with data]
	docker run -v ${dir}:${dir} lipsia vnifti -in ${dir}/output.nii -out ${dir}/output.v

margulies / index.html

Created March 14, 2020 16:25

	<!DOCTYPE html>
	<html lang="en">
	<head>
	<meta charset="UTF-8">
	<title>IPyWidget export</title>
	</head>
	<body>


	<!-- Load require.js. Delete this if your page already loads require.js -->

margulies / calculate_distance_matrix.py

Last active March 17, 2020 19:13

	import numpy as np
	import nibabel as nib
	from surfdist.load import load_freesurfer_label, get_freesurfer_label
	from surfdist.utils import surf_keep_cortex, translate_src
	import gdist
	import os

	base_dir = '/Applications/freesurfer/subjects/'
	surf = nib.freesurfer.read_geometry(os.path.join(base_dir, 'fsaverage5/surf/lh.pial'))
	cort = np.sort(nib.freesurfer.read_label(os.path.join(base_dir, 'fsaverage5/label/lh.cortex.label')))

margulies / surface_rgba.py

Created February 28, 2019 17:40

	def plot_surf_stat_multidim(coords, faces, face_colors=None, stat_map=None,
	elev=0, azim=0,
	cmap=None,
	threshold=None, bg_map=None,
	mask=None,
	bg_on_stat=False,
	alpha='auto',
	vmax=None, symmetric_cbar="auto",
	figsize=(14,11), label=None, lenient=None,
	**kwargs):

margulies / dist_calc_matrix.py

Last active August 1, 2018 15:33

function to calculate distance matrix between freesurfer labels

	import nibabel as nib, numpy as np, os, sys
	#sys.path.insert(0,'../')
	import surfdist as sd
	from surfdist import viz, load, utils

	# function to calculate distance matrix:
	def dist_calc_matrix(surf, cortex, labels, exceptions = ['Unknown', 'Medial_wall'], dist_type='min'):
	"""
	dist_type='min' or 'mean'
	returns:

margulies / vol2surf.py

Created May 25, 2017 10:37

	import nipype.pipeline.engine as pe
	import nipype.interfaces.utility as util
	import nipype.interfaces.io as nio
	from nipype.interfaces.freesurfer import SampleToSurface

	'''directories'''
	preprocDir = "/scr/adenauer1/Franz/nki_nilearn"
	freesurferDir = "/scr/ilz2/nilearn_vol2surf_wd/freesurfer"
	workingDir = "/scr/ilz2/nilearn_vol2surf_wd/"
	sinkDir = "/scr/ilz1/nilearn_vol2surf_sink/"

margulies / macaque_embedding.py

Last active November 29, 2016 21:07

	import numpy as np
	import nibabel as nib # git clone --branch enh/cifti2 https://github.com/satra/nibabel.git
	from sklearn.metrics import pairwise_distances

	# install mapalign: (comment if already installed)
	! pip install git+https://github.com/satra/mapalign
	from mapalign import embed

	# Load data and Fisher's z-to-r transform
	# load connectivity matrix as numpy array

margulies / write_cifti.py

Created November 29, 2016 11:13

	def write_cifti(data, fname, dtype = 'dscalar', labels = None, tpl = None):

	import subprocess
	import os

	assert data.shape[0] == 91282, "You must have 91282 vertices on the first dimension (rows)"

	if tpl is None:
	tpl = '/Users/marcel/projects/HCP/Connectivity_coordinate_system/rsFC_eigenvectors.dscalar.nii'

Daniel Margulies margulies