Dear Pedro,
I've just been checking through the code and the GE sequence is somewhat
confusingly related to the parameters and you cannot control the crushers,
or turn them off, which can cause problems for timing.
I assume that you want a 81.504 millisecond TE (which should be specified
as 0.081504 as all timings are in seconds, not milliseconds). However, for
a GE sequence the TRline is equal to the trslc parameter, and represents the
timing for a single line (what is usually considered the TR for a GE sequence,
and is normally about 2-3 times the TE value). The TR value specified in the
command for pulse needs to be a whole volume TR, which is the TRline
multiplied by the number of points along y (ny) and the number of slices.
So this should allow you to try and set these parameters correctly, although
the crusher time may prove to be difficult because of the crushers. The GE
sequence is still in the earlier stages of development, and hence why it is
not available via the GUI and is not totally flexible via the command line either.
I hope this helps.
All the best,
Mark
On 2 May 2011, at 16:44, Pedro Mendes wrote:
> Dear Mark,
>
> In first place I just replace the command --seq=epi by --seq=ge, as the following error appears:
>
> TR and TRline and numslc do not agree
>
>
> But I supossed that was because the TE and TR from an EPI could not be the same as an GE, so I perform the following command line:
>
> /usr/local/fsl/bin/pulse -i /usr/local/fsl/data/possum/brain.nii.gz -o /home/fsl/Desktop/possum_ge/pulse --te=81.504 --tr=9000 --trslc=9000.0 --nx=64 --ny=64 --dx=0.096 --dy=0.096 --maxG=0.055 --riset=0.00022 --bw=100000 --numvol=1 --numslc=1 --slcthk=0.0025 --zstart=0.09 --seq=ge --slcdir=z+ --readdir=x+ --phasedir=y+ --gap=0.0 -v --cover=100 --angle=90
>
> And appears the following error, again:
>
> TR and TRline and numslc do not agree
>
>
> Problably the error is in the TE,TR and TRSLC values, but I do not understand wath I am doing wrong.
>
> Best Regards,
>
> Pedro Mendes
>
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