Tim Schäfer dfsp-spirit

Bioinformatician, former Neuroscientist, and Software Developer. Currently Research Software Engineer at MPI AE.

dfsp-spirit / cmake_install_ubuntu.bash

Created July 14, 2023 09:07

Compile and install clang into user home under Ubuntu Linux

	#!/bin/sh
	#
	# This is a recipe, you should type things manually and check for errors
	# after each command instead of treating this as a fire & forget shell script.
	#
	# This follows the official clang docs at https://clang.llvm.org/get_started.html
	#
	# Done under Ubuntu 22.04 LTS, with clang fetched from Github on 2023-07-04, commit 61e0822ef.
	#
	# This does not require root, but it uses cmake. If you don't have that, building it is easy, or just use autotools.

dfsp-spirit / heat_setup_on_mpcdf_cluster.md

Last active January 20, 2023 14:38

How to install heat (for Python) on MPCDF cluster

in bash:

module load anaconda/3/2021.11
conda init bash # most likely done already.
conda create -n heat python=3.9
conda activate heat

dfsp-spirit / install_jekyll_ubuntu22_04.txt

Last active December 31, 2022 10:53

	# Installing jekyll under Ubuntu 22.04

	This was quite a pain, and I tried several things. This is a method that worked, but I do not
	have much Ruby experience and cannot tell you whether its the best method. This method uses a local ruby installation in your user directory, so it is very low-risk.

	1. Install reub-install from https://github.com/postmodern/ruby-install:

	```shell
	wget -O ruby-install-0.8.5.tar.gz https://github.com/postmodern/ruby-install/archive/v0.8.5.tar.gz
	tar -xzvf ruby-install-0.8.5.tar.gz

dfsp-spirit / test_h5py_copy.py

Created August 30, 2022 11:46

Copy hdf5 file created with python using shutil

dfsp-spirit / gist:d63a6b56f2c11c92086a81911138b453

Last active September 7, 2021 20:08

Modyfying meshes in fsbrain's interactive view using a pre-render hook

	# This currently requires fsbrain dev, >= 0.5.0.
	#
	# You will need to install with:
	#
	# devtools::install_github("dfsp-spirit/fsbrain", ref="geodesic");
	#
	# until 0.5.0 is available on CRAN.
	#

	library(fsbrain)

dfsp-spirit / fsbrain_register_post_render_hook.R

Last active August 27, 2021 15:21

	library(fsbrain)

	# We use thickness on fsaverage as demo data
	sjd = fsaverage.path();
	sj = "fsaverage";

	# Visualize once with standard settings:
	vis.subject.morph.native(sjd, sj, "thickness");

	# Register a post-render callback function that can do whatever you want:

dfsp-spirit / read_freesurfer_morph.R

Last active September 17, 2020 09:14

Reading FreeSurfer morphometry data in R

	#!/usr/bin/env Rscript
	#
	# This script illustrates how to load FreeSurfer morphometry data in R.
	#
	# If you do not have 'freesurferformats' yet, you need to install it:
	# install.packages('freesurferformats');

	library('freesurferformats');

	subjects_dir = "~/data/study1"; # Replace with your data (or with example data from the 'fsbrain' package).

dfsp-spirit / read_write_freesurfer_morph.R

Last active September 17, 2020 09:13

How to load FreeSurfer morphometry data in R, transform it and save as new file

	#!/usr/bin/env Rscript
	#
	# This script illustrates how to load morphometry data in R, apply some
	# transformation (a simple log in this example), and save the result
	# to a new file.
	#
	# If you do not have 'freesurferformats' yet, you need to install it:
	# install.packages('freesurferformats');

	library('freesurferformats');