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FSL  June 2010

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Subject:

Re: Using POSSUM in CLI

From:

Ivana Drobnjak <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Thu, 10 Jun 2010 09:20:06 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (53 lines)

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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