Hi,

The pre-processing of the fieldmap sounds fine.

The FEAT GUI is the best way to get fieldmap unwarping done as
it will do all the necessary registration steps (and some extra cleanup
of the fieldmap) for you automatically.  All you need to do is give it
your fieldmap in rad/s, the corresponding magnitude image (after
running BET on it to remove the non-brain structures) and some
parameter values (e.g. echo spacing).  It is all contained under
the "pre-stats" part and you can run it on your DTI images by
just selecting pre-stats only as the main option (top left pull-down
menu), using your DTI as the 4D input data, and turning off all the
other pre-stats options.  The output file will be called  
filtered_func_data
but will represent your distortion corrected EPI data.

That should work for you with your data.
If you have any trouble then let us know.

All the best,
	Mark



On 22 Dec 2008, at 22:19, Rajagopalan, Venkateswaran wrote:

>
> Dear All,
>
> I am new to field map correction. My field map data acquisition is a  
> single real field map image, gradient echo sequence. I have the  
> following images 1) EPI (for DTI),2)single real field map image in  
> units rad/sec and 3) the corresponding gradient echo magnitude  
> images. I went through FUGUE instruction manual and also through  
> PRELUDE documentation. There are few things which i am not able to  
> understand. I went through the field map processing steps mentioned  
> here http://www.fmrib.ox.ac.uk/fsl/fugue/feat_fieldmap.html and made  
> sure that my field map images meet the requirement for instance my  
> field map is a single real field map image registered with the  
> magnitude image (step 1b and c ), its units are in rad/sec  
> (confirmed with MR technician), i regularised them using gaussian  
> FWHM of 0.5 fugue --loadfmap=fieldmap_rads -s 1 -- 
> savefmap=fieldmap_regu. After this step i used the following FUGUE  
> command fugue -i epi --dwell=0.85 --loadfmap=fieldmap_regu -u  
> result. My first question is this approach correct.
>
> My Next question is, i have uploaded  the screenshot of my "result"  
> image  in the following link http://www.beetony.com/uploads/venk/FUGUE_result.jpg 
>  where you can see the problem, i feel that this is due to the fact  
> that field map and EPI images are not registered. I don't know  
> whether FUGUE takes cares of the registration between the gradient  
> echo field map which is of dim 63*63*30 and epi (DTI) sequence dim  
> 127*127*30 or i have to register my fieldmap by distorting it using  
> FUGUE option "fugue -i undistortedimage -p unwrappedphase -- 
> dwell=dwelltime --asym=asymtime --nokspace -s 0.5 -w warpedimage"  
> and then register the two images together and then use the following  
> FUGUE option "fugue -i epi --dwell=0.85 --loadfmap=fieldmap_regu -u  
> result" where now epi and fieldmap_regu are brought into common space.
>
> I am sorry this may be a stupid question or approach kindly help me  
> with this.
>
> Thanks in advance,
>
> venkateswaran
>
>
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