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GenwaveTutorialTutorials.GenwaveTutorial HistoryHide minor edits - Show changes to markup October 14, 2010, at 09:01 AM
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- Added a note to GEN wave tutorial about flipping the second half of the wave.Added lines 29-30:
One very important thing to remember is the The second half of the GEN wave must be multiplied by -1 with respect to the first! This mimics the actions of the 180-degree pulse. Without it, the two halves will not cancel each other out and the data synthesised will be biased and not correctly diffusion weighted. If your sequence seems correct but you are getting crazy data out of the simulation, this is probably why. June 21, 2010, at 05:22 PM
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K is the number of block in the waveform histogram\\ to:
K is the number of blocks in the waveform histogram\\ June 21, 2010, at 04:48 PM
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You're free to choose K to be whatever you like in order to specify the wave correctly. It does not need to be the same as the time increment of the simulation, any mis-match is automatically taken care of, although it is probably best to have a higher K in your waveform than the number of steps in your simulation. to:
You're free to choose K to be whatever you like in order to specify the wave correctly. It does not need to be the same as the time increment of the simulation, any mis-match is automatically taken care of, although it is probably best to have a higher K in your waveform than the number of steps in your simulation. There is no constraint on the shape of the waves, including no checking against slew rate and no constraint for pulses to be symmetric or even sum to zero -- the wave will behave exactly as you specify, right or wrong! June 21, 2010, at 04:45 PM
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You're free to choose K to be whatever you like in order to specify the wave correctly. It does not need to be the same as the time increment of the simulation, any mis-match is automatically taken care of, although it is probably best to have a higher K in your waveform than the number of steps in your simulation. Added lines 33-34:
June 21, 2010, at 04:41 PM
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Scheme files to:
Scheme files\\ Changed line 9 from:
Gen-waves to:
Gen-waves\\ Changed line 12 from:
Gen-wave scheme file format to:
Gen-wave scheme file format\\ Changed line 21 from:
Each line is formatted as follows: to:
Each line is formatted as follows:\\ Changed line 28 from:
and that's it. specify as many lines as you need, and data will be generated from a simulation in the order specified. b-zero measurements can be encoded with K=1, dt=TE and G1x etc = 0.0 to:
and that's it! specify as many lines as you need, and data will be generated from a simulation in the order specified. b-zero measurements can be encoded with K=1, dt=TE and G1x etc = 0.0 June 21, 2010, at 04:41 PM
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SYNOPSIS \\ to:
Scheme files Scheme files are what gets information about the data acquisition used in the scanner into Camino for the analysis pipeline. Different scheme file formats contain different levels of detail about what's going on as some analyses and techniques require more information than others. At a minimum, a scheme file can contain b-values and directions but some formats, particularly those used by the simulation for data synthesis, specify the pulse sequence more exactly. Gen-waves Camino contains schemes based around simple PGSE acquisitions, around Twice-refocussed acquisitions and other common pulse sequences, but as the types of pulse sequence used for diffusion imaging develop and increase in complexity, it has become necessary to have a more general format that can describe more exotic sequences. This tutorial describes the general waveform scheme format, which allows pulse sequences to be specified as three dimensional waveforms. This format allows a set of acquisitions with completely general shapes in three dimensions. As such, they are suitable for almost any pulse sequence that is not covered by the other existing waveforms. They are specifically designed to work with simulations for data synthesis. Gen-wave scheme file format Scheme files are just formatted text files and as such are human readable. The first thing to do is to create a new file in your favourite text editor with a ".scheme" extension. let's call it genwave.scheme. All scheme files start with a line specifying what format they are and gen waves are no exception. The first line of your text file should read: Each line is formatted as follows:
K dt G1x G1y G1z G2x G2y G2z ... GKx GKy GKz As with everything in Camino, all units are SI (kg, s, m). June 21, 2010, at 04:11 PM
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Tutorial: Creating a Scheme file for a general 3D waveformThis tutorial describes the general waveform scheme file format, what it describes and what the parameters mean. SYNOPSIS \\ |