POSSUM

## POSSUM Output

POSSUM creates the directory you have specified as your output directory. If you have not specified the name, POSSUM will create a directory called "simdir" in your current directory. If the directory with the name you have specified already exists , a "-" is added after the name of the old directory. Of course, all the above gets ignored if you explicitly set the output directory name.

There are two main outputs of POSSUM in the POSSUM directory:

- image_abs.nii.gz: Output image (magnitude). The image can be seen in the fslview. It is obtained from the signal (see below) after reordering it into the k-space and then reconstructing using the Discrete Fourier Transform (which can be done using a command-line program signal2image). This is already done for you within the GUI so there is no need to do it again. However, you can use signal2image yourself if you would like to get your image in a complex form, or would like to get the k-space.
- signal: Binary 2-row matrix. The most important output of POSSUM. It takes the longest to generate. It represents a raw signal (k-space data) in a similar form as the MRI scanner ouput. The first row is the data from the real channel and the second row is the data from the imaginary channel. This matrix can be seen using a MATLAB command read_pulse.m.

      signal2image

      signal2image [options] -i signal -p pulse -o image
      signal2image -p pulse -c kcoord

      Compulsory arguments (You MUST set one or more of):
              -p,--pulse      pulse_sequence matrix (generated with the GUI)

      Optional arguments (You may optionally specify one or more of):
              -i,--in         input signal (default name= signal)
              -o,--out        outputs image (default name = image)
              -c, --kcoord    kspace coordinates (default name = kcoord)
              -k,--kout       outputs k-space (default name = kspace)
              -a,--abs        save absolute magnitude and phase
              -v,--verbose    switch on diagnostic messages
              -h,--help       display this message

  The other outputs saved in the POSSUM directory are:

- signal_nonoise the same as signal just without any white (thermal) noise.
- image_phase.nii.gz output image (phase).
- image_real.nii.gz output image (real part). Can be obtained with signal2image.
- image_imag.nii.gz output image (imaginary part). Can be obtained with signal2image.
- kspace_abs.nii.gz output kspace (magnitude). Can be obtained with signal2image.
- kspace_phase.nii.gz output kspace (phase). Can be obtained with signal2image.
- kspace_real.nii.gz output kspace (real part). Can be obtained with signal2image.
- kspace_imag.nii.gz output kspace (imaginary part). Can be obtained with signal2image.
- brain.nii.gz input object.
- T2.nii.gz input 3D activation image.
- T2timecourse input activation modulation file (in time).
- b0A_dA.nii.gz input 3D B0 inhomogeneity basis set (A=x,y,z).
- pulse pulse sequence matrix (binary).
- pulse.info file with parameters of the pulse sequence (used by POSSUM programs).
- pulse.readme file with parameters of the pulse sequence (user friendly).
- pulse.posx coordinate system of the input object (x-coordinate).
- pulse.posy coordinate system of the input object (y-coordinate).
- pulse.posz coordinate system of the input object (z-coordinate).
- pulse.com command used to generate the pulse sequence.
- noise file describing the white (thermal) noise parameters with values of SNR and sigma used in the simulation (madde by the POSSUM GUI).
- motion input motion file.
- slcprof input slice profile.
- MRpar input MR parameters.
- possum.com commands used when running POSSUM (to generate signal).
- possum.fsf POSSUM setup file, describing everything about the POSSUM setup. This can be loaded into the POSSUM GUI using the command "Load".
- possum.log log file for everything that happened when you ran POSSUM GUI (except the generation of the signal which is in the logs directory).
- logs log directory which contains log files from each of the processors that generates the signal. The commands used for this are in possum.com. Files with the extension ".o" are the log files showing the process, and the files with the extension ".e" are the log files showing if there are any errors. Note that this directory is empty when there is no SGE enviroment.

  Copyright © 2007, University of Oxford. Ivana Drobnjak and Mark Jenkinson.