Hi
I will attempt to answer this, but I am passing on an answer I received
As I understand the dwell time is the time between acquisiton of
adjacent lines of the K space for the epi sequence and the asym time is
the time between the centre of the spin echo and the centre of kspace
for the field map
You can find the number to put into fugue from
extractfidparams your_epi.fid your_field_map.fid
When I did this I got 1 number out which appeared to correspond to the
dwell to assym ratio.
Credit for this answer should go to Stuart Clare and Peter Hobden - but
any mistakes in conveying it from my misunderstanding are all mine.
Harriet
Jane Aspell wrote:
>Dear Steve (and FSL list)
>
>Thanks for the advice for improving my registration. I am trying to run the
>fieldmap correction as Steve suggested and have run prelude with the line:
>
>prelude -c series_2_b0map -u unwrapped phase
>
>which generated unwrapped.hdr and .img files, but i am have trouble figuring out
>the correct command to run fugue. the website suggests various forms of usage.
>would the following be correct?...
>
>fugue -i epi -p unwrappedphase -d dwell-to-asymratio -s 0.5 -u unwarped_epi
>
>how do i find out what my dwell-to-asymratio is?
>
>and once this has created the unwarped_epi.hdr/img file can i use it in place of
>the epi it was created from or do i carry out an extra stage of registration of
>the warped to unwarped epi? it's just not very clear in the online documentation
>what the sequence should be.
>
>thanks so much for your help,
>
>Jane Aspell
>
>
>
>
>
>
>In message <[log in to unmask]> FSL -
>FMRIB's Software Library <[log in to unmask]> writes:
>
>
>>Hi - this all looks fine. It looks like the registrations are fine and the
>>small areas where the activation "leaves" the brain are probably due to a
>>combination of smoothing, and slight distortions between the EPI data and
>>the T1 structural.
>>
>>You might get slightly better registration of the initial highres to the
>>main structural (the "main structural image" registration part of the GUI)
>>if you correct the initial highres with fieldmap correction, or, failing
>>that, use 12 DOF in this second stage of the registration.
>>
>>Cheers.
>>
>>
>>
>>On Fri, 21 May 2004, Jane Aspell wrote:
>>
>>
>>
>>>Hi Steve
>>>I've put my feat directory of a first level feat analysis of one run on
>>>cayenne:
>>>/usr/fs5/aspell
>>>
>>>it's a tarred zipped directory called
>>>2ndseries2.2.feat.tar.gz
>>>
>>>in it is also a folder called /highes_reg which contains the T1 image
>>>(struct.hdr) for the
>>>subject and a single stats image that i have registered to it with flirt -
>>>2ndser2.2reg_shadowreg_cluster_mask_zstat1.hdr
>>>
>>>...just to give you an example of what i mean.
>>>
>>>thanks again for the help
>>>jane
>>>
>>>
>>>In message <[log in to unmask]>
>>>FSL - FMRIB's Software Library <[log in to unmask]> writes:
>>>
>>>
>>>>Hi - no, FLIRT will have corrected for the different voxel sizes - if the
>>>>registration overlays look ok then any weird looking stuff in the
>>>>activation overlays can't be due to registration-related issues. It might
>>>>be worth you putting the full FEAT directory on a website so we can have a
>>>>look at the effects you are worried about.
>>>>
>>>>Cheers, Steve.
>>>>
>>>>
>>>>On Wed, 19 May 2004, Jane Aspell wrote:
>>>>
>>>>
>>>>
>>>>>Steve,
>>>>>some more points to add to the previous query...even though the
>>>>>registration page on the feat report looks ok my activations on highres
>>>>>overlay doesn't. i wondered if the problem might be a failure to match
>>>>>pixel sizes in the different images. for one subject both 24 slice
>>>>>functional EPI and 120 slice EPI ('initial sturctural') have pixdims
>>>>>3,3,3 but for another subject the 120 slice is 4,4,3. i don't know why
>>>>>the latter is different for one of the subjects. could this difference
>>>>>between the 24 slice and 120 slice image for one of the subjects be
>>>>>causing a problem? and do i need to set some parameter (eg one of the
>>>>>advanced options) in flirt to allow for the fact that my 24 slice
>>>>>functional EPI (and 120 slice EPI) has slices at an oblique angle?
>>>>>thanks for your help
>>>>>
>>>>>Jane
>>>>>
>>>>>
>>>>>
>>>>>In message
>>>>><[log in to unmask]> FSL
>>>>>- FMRIB's Software Library <[log in to unmask]> writes:
>>>>>
>>>>>
>>>>>>Hi - it's difficult to judge registration quality by looking at the
>>>>>>activation overlay - you should be clicking on the registration
>>>>>>evaluation image towards the bottom of the FEAT webpage report and
>>>>>>look at the detailed registration evaluation images - do they look ok?
>>>>>>
>>>>>>
>>>>>>Cheers, Steve.
>>>>>>
>>>>>>
>>>>>>On Mon, 17 May 2004, Jane Aspell wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>>>Hi
>>>>>>>
>>>>>>>I'm having some problems registering my functional data onto a highres
>>>>>>>image of an individual subject's brain. My functional data is in the
>>>>>>>form of 24 obliquely oriented slices mainly covering the occipital
>>>>>>>area (it's a vision study). The clusters of activation seem to 'flame
>>>>>>>out' from the brain in some areas, into 'space' by a few millimetres.
>>>>>>>This problem seems to be worse in occipital areas and not so bad in
>>>>>>>parietal areas. I have an idea that occipital areas are subject to
>>>>>>>more distortion than other areas - is this true? To register my
>>>>>>>functional to a highres with flirt i did a 7 parameter global rescale
>>>>>>>transformation from my 24 slice functional data to a 120 slice EPI
>>>>>>>(slices at the same angle as the functional) and another 7 param
>>>>>>>global rescale to my individual highres structural. is there anything
>>>>>>>you could advise i do to improve my registration?
>>>>>>>
>>>>>>>many thanks for your time,
>>>>>>>
>>>>>>>Jane Aspell
>>>>>>>
>>>>>>>
>>>>>>>
>
>
>
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