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Subject:

Re: Field maps and Registration

From:

Jane Aspell <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Mon, 7 Jun 2004 12:29:04 +0100

Content-Type:

text/plain

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text/plain (194 lines)

Thanks Harriet - I am able to get a number out as you advise. Do you know - or
can anyone else advise - if, once I have then created the unwarped EPI with
FUGUE I can use the resulting file in FEAT (in place of the previously distorted
one it was generated from), or do I need to carry out any further steps before I
do that?

best,

Jane



In message <[log in to unmask]> FSL - FMRIB's Software Library
<[log in to unmask]> writes:
> 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
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >
> >
> >
>

--
Dr Jane Aspell
Department of Experimental Psychology, University of Oxford,
South Parks Road, Oxford, OX1 3UD
tel: +44 (0)1865-281606

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