Dear Martin,

Almost right....

First things first - prelude comes before fugue (hence the name!)

You run prelude to unwrap the phasemaps that constitute your
fieldmap acquisition data (assuming the scanner software didn't
do it for you).  Once you've done this and made your fieldmap
(ideally in units of rad/s, Hz or T) then you've finished with prelude.

After prelude you run fugue in several stages.  The first is to create
a *warped* magnitude image (of the fieldmap) - note, warped, not
wrapped.  This is then registered to the EPI image (which it should
match in distortions), allowing the fieldmap to be resampled to the
EPI space.  Once this is done, fugue is run again, this time in unwarp
mode to create an unwarped EPI.  This unwarped EPI is then used
as the input in registration with the structural.

This is the basic setup, although weighting the cost function for
estimated signal loss is also important.

The new release of FSL will contain automated unwarping within
FEAT.  So if you wait for a week or two then you should be able to
grab the newest release and run it more easily through the FEAT
GUI.  However, it is still useful to understand the process and be able
to interpret the images that will appear in the FEAT report.

As for unwarping direction, this should be the *phase encode* direction
of your images.  I cannot tell you whether z is the correct direction  
for
you or not as it completely acquisition dependent and often changed
for different scanners/sites/experiments.  One thing I can tell you  
is that
it is *not* the slice direction.

All the best,
	Mark


On 20 Mar 2006, at 22:00, Martin M. Monti wrote:

> Hi,
>
>  I've been reading (and re-reading, and re-re-reading) the few  
> pages online re unwarping EPIs with field maps but I would like to  
> run by you my understanding of the whole thing to see if I am  
> correctly understanding the procedure.. I'll try to make this as  
> short and bullet-point as possible to speed up reading.. :)
>
> Consider - for example - starting with a (non-BET extracted) EPI,  
> and a low-res (with same #of slices as the EPI) fieldmap_phase  
> image and fieldmap_magnitude image (i.e. the absolute).
>
> 1) Create Forward-Wrap image for registering with EPI [FUGUE]
> [e.g. fugue -i fieldmap_mag -p fieldmap_phase -d dwell/asym -w  
> forward_wrap -v]
>
> 2) Register the Forward_wrap image to EPI [FLIRT]
> [e.g. flirt -in forward_wrap -ref EPI -out forward_wrap_reg -omat  
> invol2refvol.mat -dof 6]
>
> 3) Unwrap the fieldmap_phase images using the previously registred  
> (in step #2) forward_wrap_reg [PRELUDE]
> [e.g. prelude -a forward_wrap_reg -u unwrapped_fieldmap_phase_reg]
>
> 4) Unwarp the EPI with the unwrapped (in step #3) and registered  
> (in step #2)  field phase map [FUGUE]
> [e.g. fugue -i EPI -p unwrapped_fieldmap_phase_reg -d dwell/asym -s  
> 0.5 -u unwarped_EPI]
>
> Next use BET and proceed to a normal analysis (e.g. FEAT fist- &  
> higher- levels analysis) using unwarped_EPI as the functional data  
> in lieu of the original EPI.
>
>  Is this a correct interpretation of the Prelude/Fugue un- 
> distortion procedure?
>
> One lingering question: standard direction of unwarping is "y",  
> should this be set to reflect my specific acquisition direction  
> (e.g. z)?
>
> Hope this is clear enough to spot my mistakes..
>
>  Many thanks for the continuous help (it's so good that I just keep  
> wanting more..)
>
>  Cheers
>
>  Martin
>
>
>
> PS: still working on the peri-stimulus plot [...sorry I'm this hard!]
>
>
>
> --------------------------
> "Upward, not Northward!" [Edwin Abbott - FlatLand]
>
> I became insane, with long intervals of horrible sanity. [E.A. Poe]
>
> Would you tell me, please, which way I ought to go from here?  
> ''That depends a good deal on where you want to get to.'' Said the  
> Cat. I don't much care where -- Said Alice. Then it doesn't matter  
> which way you go, said the Cat. [Lewis Carroll]
>
> Che si trattasse di una gara? ..Un colpo il mondo e un colpo tu, a  
> chi stupiva un po' di piu'.. [Per Un Vecchio Bambino - Roberto  
> Vecchioni]
>
> --------------------------------------------
> Martin M. Monti
> Princeton University
> Department of Psychology
> Green Hall 3-S-8
> (609) 258-5679
> www.webmartin.net
> --------------------------------------------
>