Hi,
thanks for the advices. I am not using any of the default files except
MRpar_T3. All data included to the simulation is our own. The motion is
defined for every timepoint in the simulation and so I need all b0 files
to the input.
So, if I have the b0 files created from the air-tissue-segmentation by
the instructions you have in the Possum home page (b0calc + fslmerge), I
need them and the b0 4D map as an input to the simulator?
The GUI asks about the units of the b0 field, where this is defined in CLI?
Ivana Drobnjak wrote:
> Hi Juha,
>
> 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,
> Best ,
> Ivana
>
>
>
> On 9 Jun 2010, at 14:40, Juha Pajula <[log in to unmask]> wrote:
>
>> Hi!
>>
>> 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
>>
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