Hi Mark,
Thanks for the suggestions and the outline of the process.
Just to give you some background, Doug and I are working
on defining field map correction analysis pathways using prelude
and fugue to be be used as part of the fBIRN, a multi-center study here
in the US. We will be defining pathways for Siemens (Doug) and GE
(me) sites, so as Doug mentioned, any feedback is appreciated.
Thanks again,
Tom
*On Jun 7, 2004, at 10:00 AM, Doug Greve wrote:
> Hi Mark,
>
> I've been talking with Tom off-line about this, and here's the solution
> that we came up with. I just thought I'd post it in case anyone had any
> feedback for us.
>
> thanks
>
> doug
>
>
> 1. Compute the voxel shift map from the B0 map in the highres space
> (using prelude/fugue).
> 2. Align (motion correct) the functional run to the middle time-point
> (using mcflirt)
> 3. Register the B0 magnitude to the middle time-point (flirt)
> 4. Resample the voxel shift map to the middle time-point based on the
> registration. This handles the high-to-low res conversion. (flirt)
> 5. B0 correct (ie, run fugue) on all time-points of the motion
> corrected
> functional based on the resampled voxel shift map.
>
>
> Mark Jenkinson wrote:
>>
>> Hi,
>>
>> Sorry I haven't replied sooner but I haven't tried this before so I
>> needed
>> to have a close look at the code. Unfortunately, there is a place in
>> the
>> code where it assumes the field map and EPI are the same size so you
>> can't simply use it as you'd like for now. I will update the code to
>> make
>> it more flexible and the next release (probably in a few months' time)
>> will have this new version.
>>
>> In the meantime the easiest work around is to down-sample your
>> field maps to make them 64x64. I know this isn't ideal but it is easy
>> to do and will work pretty well. To do the down-sampling just use
>> flirt with something like:
>> flirt -ref epi -in fmap -out fmap64 -applyxfm
>> This applies a small blurring prior to applying the transformation in
>> order
>> to maintain information from all voxels in the down-sampling, and will
>> output
>> a fieldmap (fmap64) which is the same size as the epi, without any
>> spatial
>> transformation (the default transform for -init is the identity
>> transformation).
>>
>> Then use fugue with the epi and fmap64.
>> Note that flirt doesn't work with complex images, so make sure
>> the fmap image used above is either the output from fugue with
>> the --savefmap option, or the output from prelude.
>>
>> Also note that it assumes that the images fmap and epi are registered.
>> Ideally you should down-sample, forward warp the magnitude image
>> from the field map sequence, register this warped image with the epi
>> and then apply the transformation to fmap in order to have it properly
>> registered with the epi. See the information at
>> http://www.fmrib.ox.ac.uk/fslcourse/flirt_fugue
>> for more on this.
>>
>> Hope this does the trick for now.
>> All the best,
>> Mark
>>
>> On Thursday, June 3, 2004, at 08:53 pm, Tom Liu wrote:
>>
>>> Hi,
>>>
>>> We are starting to look at the use of PRELUDE and FUGUE for
>>> unwarping of DICOM EPI images off a GE 3T short bore, and had
>>> a quick question: How does FUGUE handle higher resolution field maps?
>>> e.g. if we acquire 128x128 map, will FUGUE properly apply it to a
>>> 64x64
>>> EPI image? Our initial tests seem to indicate that it sort of works,
>>> but I haven't
>>> seen anything in the documentation or lists indicating that it
>>> should.
>>> The reason I ask is that the standard SGPR that we're planning
>>> on using seems to have a silly lower limit of 128x128, and we'd
>>> rather
>>> not
>>> modify the product code unless we have to.
>>>
>>> Thanks,
>>>
>>> Tom Liu
>>>
>>> ***********************************************************
>>> Thomas Liu
>>> Center for Functional Magnetic Resonance Imaging
>>> University of California, San Diego
>>> 9500 Gilman Drive, Mail code 0677
>>> La Jolla, CA 92093
>>> Phone: (858) 822-0542
>>> Fax: (858) 822-0605
>>> http://fmriserver.ucsd.edu/ttliu
>>> ***********************************************************
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> [log in to unmask]
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
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