Tim Schäfer dfsp-spirit

## cmake_install_ubuntu.bash
#!/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.

## heat_setup_on_mpcdf_cluster.md

      
              1 file
            
          
              0 forks
            
          
              0 comments
            
          
              1 star
            
          
                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

  
## install_jekyll_ubuntu22_04.txt
# 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

## test_h5py_copy.py
#!/usr/bin/env python

import h5py
import shutil
import numpy as np
import os

filename = "test.h5"
copy_filename = 'test_cpy.h5'

## gist:d63a6b56f2c11c92086a81911138b453
# 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)

## fsbrain_register_post_render_hook.R
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:

## read_freesurfer_morph.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).

## read_write_freesurfer_morph.R
#!/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');
	#!/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.
	# 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
	#!/usr/bin/env python

	import h5py
	import shutil
	import numpy as np
	import os

	filename = "test.h5"
	copy_filename = 'test_cpy.h5'
	# 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)
	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:
	#!/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).
	#!/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');