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MRTwin_pulseq in the FAU CIP pool

Installation and starting Spyder in the FAU-CIP pool

you can clone the current version into your home folder by opening a terminal in the home folder and run:

git clone -b mr0-core https://github.com/mzaiss/MRTwin_pulseq.git --depth 1

Installation of MRTwin_pulseq

The cip-quota for disk space is limited, thus we need to make a symlink to the more relaxed /proj directory. We do thsi for the python package installation folder site-packages. This is done in the first 4 commands, the other 7 install packages an a specific environment python3/anaconda-2022.05

Run all of the following commands in a terminal:

mkdir /proj/ciptmp/$USER/
mv /home/cip/guests/$USER/.local/lib/python3.9/site-packages/ /home/cip/guests/$USER/.local/lib/python3.9/site-packages-backup
ln -s /proj/ciptmp/$USER/site-packages /home/cip/guests/$USER/.local/lib/python3.9/site-packages
mv /home/cip/guests/$USER/.local/lib/python3.9/site-packages-backup /proj/ciptmp/$USER/site-packages

module load python3/anaconda-2022.05
pip install mrzerocore
pip install pypulseq==1.3.1.post1
pip install torchkbnufft==1.3.0 --no-deps
pip install scikit-image
pip install PyWavelets

Start spyder

After running the installation you can start the environment by running in any terminal:

module load python3/anaconda-2022.05
spyder

Check the installation

See if you can run the python files ex/ex_help_01_python and ex/exB05. If errors occur check the versions of the required packages. Or get help from the admin.

General recommended settings in Spyder

To have plots as separate window, which allows resizing and zooming, go to Tools->Preferences. Then on the rider IPythonKonsole go to Graphics and choose for the graphics backend: Automatic. Then you have to close and restart spyder.

I recommend to switch the layout to matlab layout. G to View->Layouts -> Matlab Layout or Rstudio Layout.

Diff tool

If you want compare changed files or sample solutions you can use the tools diff, or more visually advanced Kompare or Meld.

useful terminal commands:

arandr : screen position/projector

quota and large files

cip-quota

ncdu

du -a |sort -n -r | head -n 20

pip cache purge

git

git clone https://github.com/mzaiss/MRTwin_pulseq.git

git pull

git difftool --tool kompare

git diff (press q to leave) git diff --name-only