The reason is to resacle the image to radians from the scale that Siemens outputs the images in.
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Lee Dongha
Sent: Monday, November 09, 2009 5:36 PM
To: [log in to unmask]
Subject: Re: [FSL] EPI Distortion Correction Queries...
Dear Matt,
You mentioned
<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. >
Why is it correct?
I don't know why substract 4096 and divide by 4096 when image from
siemens scanner is scaled from -4096 to 4096.
cheers,
dongha
[log in to unmask] 쓴 글:
>
> 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]>
>
>
>
>
>
> 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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> registered address of GlaxoSmithKline Services Unlimited
> is 980 Great West Road, Brentford, Middlesex TW8 9GS.
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> This e-mail was sent by GlaxoSmithKline Services Unlimited
> (registered in England and Wales No. 1047315), which is a
> member of the GlaxoSmithKline group of companies. The
> registered address of GlaxoSmithKline Services Unlimited
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