This repository contains quick-and-dirty utility scripts for Bruker scanning
Experimentally, we have discovered that the sequence only detects the files if:
- Main orientation file Dir.dat need to have EXACTLY 6 decimal digit
- The points in the waveform file need to STRICTLY have norm < 1 with the decimal truncation.
- Waveform file cannot have extension (need to remove the .gp)
Also,
- Waveform files need to be in /opt/PV6.0.1/prog/curdir/USER/ParaVision/exp/lists/gp
- only "-" and "_" special characters are allowed.
make_waveform.m is a very very very slightly modified version of Daniel Topgaard Gradient waveforms for axisymmetric b-tensors code.
make_waveform.py is a commandline wrapper around make_waveform.m using oct2py.
make_waveform.py 0.66 0.01 sph /home/user/schemefile/ sphericalRAW.gp -p
to generate and plot a spherical b-tensor waveform with gmax = 0.66 T/m and a duration = 0.01 s and saving it as /home/user/schemefile/sphericalRAW.gp
fix_gp_norm.py is a heuristic script that fixes the waveform points that have norm above one (because of decimal truncation)
fix_gp_norm.py /home/user/schemefile/sphericalRAW.gp /home/user/schemefile/spherical
guess_tau_from_b.py is a heuristic utility script to guess the correct waveform duration (tau) from the desired maximum gradient strenght and the target b-value (careful with units)
guess_tau_from_b.py 1 0.66
>> 14.842199577008097
So a 14.84 ms waveform with gmax = 0.66 T/m will have a b-value of 1 ms/um^2
guess_G_from_b.py is a heuristic utility script to guess the correct gradient strenght from the desired waveform duration and the target b-value (careful with units)
guess_G_from_b.py 1 14.84
>> 0.660146742717
So a 14.84 ms waveform with gmax = 0.66 T/m will have a b-value of 1 ms/um^2
fslbvec2budde.py converts a fsl bvec file into a compatible Dir.dat file without touching any of the vectors norm (assumes all norms = 1)
fslbvec2budde.py bvec.txt /home/user/schemefile/ dir.dat