Hello,
Did you use MPI parallelisation environment when you were compiling/running POSSUM or you just used the scripted version through either using the command line or POSSUM GUI? If you did use the GUI it would be useful to see the saved posum.fsf file. You could just send it to me off-line to [log in to unmask]
Your TR value, TRslice value and the number of slices do not agree. Usually POSSUM gives an error message when that happens. Could you also please check and let me know what is written in your possum.log file and your logs directory any of the .o files.
Flashing at volume 0 is due to the saturation effects - a standard MRI feature - the first volume has the highest M0 value. After that the Mz component does not fully recover to its maximum possible value.
Best,
Ivana
On 6 Dec 2012, at 19:49, Ying Wang <[log in to unmask]>
wrote:
> Dear FSL experts,
>
> I run POSSUM simulation in High performance computer center (hpcc). When I view the final result (image_abs.nil.gz) in fslview, the image is not a whole brain but 12 slim slices. I guess that it may be caused by parallel computation, since I get a whole brain image when using one CPU. I did the simulation by using parallel computing (12 CPUs). I do not know how to integrate them and make it look like a whole brain. Does anyone know how to solve this problem?
>
> Another question is when I view the final result (image_abs.nil.gz) in fslview by using movie mode, it always flashes at volume 0, no matter how many volumes it has. Is it a common phenomenon?
>
> I listed my parameters as below for reference. Thank you very much in advance.
>
> TE: 0.03s
> TR: 2.5s
> TRslice:0.078s
> Number of Voxels: 64*64*64
> Voxel size: 3*3*3
> k-space: 100
> flip angle: 90
> number of volume: 20
> gap:0
> BW: 143360
> echo spacing: 0.000571
> starting slice:0
>
> Scanner properties:
> maximal gradient strength: 0.04
> rise time:0.00015
>
> B0 Field:3T
>
> Motivation: none
>
> Activation:T2
>
> Noise: none
>
> Sincerely,
> Ying Wang
>
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