Dear Matt,
Thank you for your advice.
I have a question.
I'd like to convert radians to mm
Is is possible to use above equations?
Frequency = Velocity / waveLength
V=3*10^8 // radio wave velocity
1 rad/s = 1/(2*pi) Hz
L = V / F = 2*pi*3*10^8 / F' (m) // F'=F*1 rad/s
L = 2*pi*3*10^11 / F (mm)
Cheers,
Dongha
Matt Glasser 쓴 글:
> 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 in England and Wales No. 1047315), which is a
>> member of the GlaxoSmithKline group of companies. The
>> registered address of GlaxoSmithKline Services Unlimited
>> is 980 Great West Road, Brentford, Middlesex TW8 9GS.
>> -----------------------------------------------------------
>> -----------------------------------------------------------
>> 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
>> is 980 Great West Road, Brentford, Middlesex TW8 9GS.
>> -----------------------------------------------------------
>>
>>
>
>
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