The best command line to use in order to get the full and thorough
description of all the options is possum. PossumX is the wraper , and
the pulse is for sequence generation .
When you do not have motion the best is just to use b0 map. However
when you have motion you also need b0x , b0y and b0z. You can use
program b0calc to calculate them together with the b0 map. If you are
using a phantom provided with FSL (default phantom in possum) you do
not have to calculate them your self , they are already calculated and
are part of the full b0. If you just include that file in your possum
directory when running possumx, the code will recognize it
automatically ( as long as you are using the same name).
PossumX is really essy to run . It is applied on a directory and the
run is determined with what is in that directory. It is only important
to name the files in the directory in a way that they can be
recognized e.g. Motion file is called motion , sequence file is called
pulse and so on . The list of names is given in the possumx help
lines, and the already generated files are stored in fsl/data/possum
Hope this helps,
On 9 Jun 2010, at 14:40, Juha Pajula <[log in to unmask]> wrote:
> Do you have any kind of instructions how tho use POSSUM simulator in
> command line interface. I need the 4D activation sequence in the
> simulations so I cannot use the GUI. The use of the pulse and the
> possumX commands looks simple, but some inputs are unclear for me.
> For example, how the b0 inputs for possumX are defined? What is the
> difference between basic b0 and full b0. When I have the motion case
> do I need to create the b0x_dx ... b0z_dy files by myself and if it
> is so how do I do it?
> Is there something else I need to get considered when I am using the
> possum in command line?
> Juha Pajula,
> Research Assistant,
> Methods and Models for Biological Signals and Images group of Signal
> Processing department in Tampere University of Technology