Hi,
I agree with what Matt has said.
We need to know what the FOV is for your EPI and fieldmap, not just
the number of slices. Note that FOV = (number of slices) * (slice
thickness)
If that is similar and covers most of the brain then you do not need
to worry
about partial FOV registration. Otherwise if they are different then
you probably
should.
All the best,
Mark
On 9 Nov 2009, at 17:18, [log in to unmask] wrote:
>
> :) in any case, thank you!!
>
> cheers,
> ying
>
>
>
> "Matt Glasser" <[log in to unmask]>
> Sent by: "FSL - FMRIB's Software Library" <[log in to unmask]>
> 09-Nov-2009 16:57
> Please respond to "FSL - FMRIB's Software Library"
> <[log in to unmask]>
>
>
>
> To
> [log in to unmask]
> cc
> Subject
> Re: [FSL] EPI Distortion Correction Queries...
>
>
>
>
>
> Well, so long as the field map FOV includes all of the EPI FOV, it
> should be possible to correct. As for how to deal with the partial
> volume registration, that would be a question for someone more
> knowledgeable like Mark. J
>
> Peace,
>
> Matt.
>
>
>
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf Of [log in to unmask]
> Sent: Monday, November 09, 2009 10:52 AM
> To: [log in to unmask]
> Subject: Re: [FSL] EPI Distortion Correction Queries...
>
>
> Dear Matt,
>
> I see. I've had some problems unwarping a set of partial volume EPI
> images. Initially, i thought it might have been due to the
> orientation. If that's the case, i guess the difference in number of
> slices between the fieldmaps (which have 46 slices) and the EPI that
> i'm trying to correct (which has 26 slices) could possibly cause a
> problem during the registration of the fieldmap magnitude to the EPI?
>
> I've read somewhere on the fsl website about registering the partial
> FOV to a full brain EPI.. Would that help?
>
> cheers,
> ying
>
>
> "Matt Glasser" <[log in to unmask]>
> Sent by: "FSL - FMRIB's Software Library" <[log in to unmask]>
> 09-Nov-2009 16:19
>
>
> Please respond to "FSL - FMRIB's Software Library"
> <[log in to unmask]>
>
>
>
>
> To
> [log in to unmask]
> cc
>
> Subject
> Re: [FSL] EPI Distortion Correction Queries...
>
>
>
>
>
>
>
>
>
>
>
>
> No that should not matter, as the magnitude of the field map will be
> registered to the fMRI. However, the field map should include the
> whole fMRI volume in its FOV or the parts outside will not be
> corrected.
>
> Peace,
>
> Matt.
>
>
>
>
>
>
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf Of [log in to unmask]
> Sent: Monday, November 09, 2009 9:08 AM
> To: [log in to unmask]
> Subject: Re: [FSL] EPI Distortion Correction Queries...
>
>
> Dear Matt,
>
> Thank you very much for your reply..
>
> Do you think it would be a problem if the EPI image is not in the
> same orientation (as in if you look at the sagittal plane, it's not
> tilted the same way) as the gradient fieldmaps?
>
> cheers,
> ying
> "Matt Glasser" <[log in to unmask]>
> Sent by: "FSL - FMRIB's Software Library" <[log in to unmask]>
> 22-Oct-2009 16:38
>
>
>
>
> Please respond to "FSL - FMRIB's Software Library"
> <[log in to unmask]>
>
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> To
> [log in to unmask]
> cc
>
> Subject
> Re: [FSL] EPI Distortion Correction Queries...
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> 1) Are these from a Siemens scanner? If so, the procedure looks
> correct, though I would check the original phase image range to see
> if how it is scaled. If it is scaled from 0 to 4095, then what you
> have is correct. If it is scaled from -4096 to 4096, then you need
> to subtract 4096 and divide by 4096.
>
> 2) That sounds like a good way of determining whether the unwarp
> direction is y or y-. You can try registering the images to an
> undistorted anatomical image to more clearly see which one is
> correcting the distortion and which one is making it twice as bad.
>
> 3) I would do the MCFLIRT and then compare vs the undistorted
> structural
>
> Peace,
>
> Matt.
>
>
>
>
>
>
>
>
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf Of [log in to unmask]
> Sent: Thursday, October 22, 2009 6:19 AM
> To: [log in to unmask]
> Subject: [FSL] EPI Distortion Correction Queries...
>
>
> Dear Sir/Madam,
>
> I have been trying to work with EPI Distortion correction in
> accordance to the documentation as follows: http://www.fmrib.ox.ac.uk/fsl/fugue/index.html
> , http://www.fmrib.ox.ac.uk/fslcourse/ (lecture and practical).
> However, i am unsure if i've understood them correctly, and was
> hoping you would be kind enough to provide me with some advice.
>
> 1) i'll have two magnitude images (one from each TE, 5ms vs 8ms) and
> one phase difference image from the scanners. And i would prepare
> them as follows:
>
> # to bet the magnitude image
> standard_space_roi {mag_5ms} premask -b
> bet2 premask mag_brain -f 0.4
>
> # to convert phase image to radians/s
> fslmaths {phase_diff} -sub 2048 -div 2048 -mul 3.14159 rad_phase -
> odt float
> prelude -p rad_phase -a mag_brain -o urad_phase
> fslmaths urad_phase -div 0.00246 urads_phase
>
> 2) then within FEAT, using the B0 unwarping option alone, i'd input
> mag_brain as the magnitude image, and urads_phase as the phase
> image, and try both y and -y to figure out which direction is better.
>
> 3) According to our physicist, the direction of distortion should be
> posterior towards anterior. In order to figure out whether the
> unwarp was an improvement:
>
> - i would compare examplefunc vs example_func_orig_distorted and see
> which regions (with special attention to frontal, inferior temporal
> regions) to see whether they were shifted more anteriorly with
> unwarping
> - i would look at the example_func2highres vs
> example_func_orig_distorted2highres to see which has a better
> registration with the highres (this is especially challenging as i
> can only judge using the ventricles as the cortical areas are
> difficult to judge)
>
>
> My queries would be:
> 1) Does the preparation of the gradient echo images sound correct?
> 2) Do the methods of deducing whether there was an improvement make
> sense? If not, are there other ways of doing so, such as judging
> from the feat report EPI correction section?
> 3) Would it make sense to do a comparison by (a) applying unwarp to
> the EPI alone, or (b) with the rest of the preprocessing e.g MCFLIRT
> etc, (c) within subject, or across subject (on a group level) to be
> able to judge if unwarp has caused an improvement?
>
>
> Your help would be immensely appreciated. Looking forward to hear
> from you.
>
> Yours faithfully,
> Ying
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> This e-mail was sent by GlaxoSmithKline Services Unlimited
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