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Subject:

Re: Registration woes

From:

"Fornito, Alexander" <[log in to unmask]>

Reply-To:

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

Date:

Mon, 18 Oct 2004 15:45:30 +1000

Content-Type:

multipart/mixed

Parts/Attachments:

Parts/Attachments

text/plain (265 lines) , fsl_alef_fornito.tar.gz (265 lines)

Hi Mark,
We don't have a web page or ftp running at the moment, but I've attached
the initial highres (wholehead epi), highres (that subject's axial T1)
and the weight I created to downweight the signal loss as a compressed
tar file (< 1M). Hope this is ok.
Appreciate all your help!
Alex 

-----Original Message-----
From: Mark Jenkinson [mailto:[log in to unmask]] 
Sent: Friday, October 15, 2004 3:28 PM
To: [log in to unmask]
Subject: Re: [FSL] Registration woes

Hi Alex,

OK, sounds like you have done the sensible things.
Could you put your images and weighting volumes somewhere
for us to download (web page or ftp)?
We'll take a look at them at this end and see if there
is anything that can be done.

All the best,
        Mark



On Fri, 15 Oct 2004, Fornito, Alexander wrote:

> Hi,
> Thanks for your help - it's clarified a few things. However, I'm still
> having a bit of trouble. Maybe you can tell me where I'm going wrong.
> I've done what you suggested, trying to create a weight in the input
> space.
> I drew a mask around there areas of signal loss (orbital frontal and
> inferior temporal areas) and saved this out as a binary image file (in
> analyze format), with the mask valued at 0 and the rest (including
> non-brain) as 1. I then included this image as the input weight using
> the flirt GUI when registering the epi to the subjects T1, but it
> appears to have made little difference to the actual registration.
> I then tried again, this time drawing a mask around the ventricles and
> weighting them as 2, the signal dropout as 0, and the rest as 1, but
> again, there appears to be little difference in the registration
> results.
> Am I missing something?
> Thanks again,
> Alex
>
> -----Original Message-----
> From: Mark Jenkinson [mailto:[log in to unmask]]
> Sent: Friday, October 01, 2004 10:27 PM
> To: [log in to unmask]
> Subject: Re: [FSL] Registration woes
>
> Hi Alex,
>
> I agree with Tim.  Especially in that it is very important to
> distinguish
> masking from weighting - they are quite different operations.
>
> I would say that there isn't much advantage in smoothing the cost
> weights
> though, so you could easily ignore that step.
>
> Also, I never recommend drawing weights based on a non-weighted
> registration
> (using mricro's linked view or anything else) as it is only likely to
be
> much good
> if the registration is good, which is not going to be true when you
> really need
> the weights the most.  Either draw it directly on the functions where
> you can
> see the signal loss (and use the -inweight) or draw a general one in
the
> appropriate
> areas on a structural or standard-space image (and use the -refweight
> option).
> The latter saves a lot of time if you are doing this many times on
> different
> scans.
>
> It is also worth noting that the larger the ignored area in the
weights
> (voxels
> with zero or near-zero values) then the less robust the initial search
> phase of
> the registration becomes.  So for weights with relative large areas
> being set
> near zero it is best to use "no search" either via the GUI pull-down
> options
> or by using -nosearch in the command line.  This will then require
that
> the
> initial positions of the images are no more than say 20-30 degrees out
> of
> alignment, but as long as the slicing (sagittal, axial, oblique, etc)
is
> the same
> or can be made the same (or nearly the same) using avwswapdim then
> there should be no problems.
>
> Hope this is also useful.
>
> All the best,
>     Mark
>
>
>
> Tim Behrens wrote:
>
> >Hi Alex,
> >
> >I'll have a go at answering these - Mark can correct me when I get it
> >wrong..
> >
> >
> >
> >>1 - Would I have to mask just the initial highres, or both the
initial
> >>highres and task epi? If the latter, would I just mask the middle
> volume,
> >>as this is what is used in the registration? If so, my 4D file
> contains
> >>160 volumes. Would the middle correspond to the 79th, or the 80th?
> >>
> >>
> >
> >the cost function mask is a separate 3D image in reference
(-refweight)
> or
> >input (-inweight) space ( you can actually apply both weightings if
you
> >like, but they have to be in the right spaces). Note that Cost
function
> >weighting is different from masking the original images, as masking
> >introduces artificial edges which will drive the registration -
usually
> >not a good idea.
> >
> >
> >
> >
> >>2 - The CBU page recommends co-registering the epi to the structural
> and
> >>using the "yoke" function in MRIcro to identify points where there
is
> >>signal dropout in the epi relative to the structural. These are the
> >>portions that should be masked out. If I register the unmasked epi
to
> the
> >>structural, wouldn't this yield a (relatively) poor correspondance
> between
> >>the images, so that using this as the basis for identifying signal
> dropout
> >>would not be the best way to go about it? Are there any alternative
> ways
> >>for idetifying which areas to mask out?
> >>
> >>
> >>
> >
> >If you use -inweight, your cost function weight mask will be directly
> in
> >input space so you can just downweight the areas with susceptibility
> >artefact, and upweight the boundaries you trust ( lateral walls of
the
> >ventricles etc.. ). If you wanted to you could apply a _generic_ MNI
> space
> >mask to the reference space (-refweight) which would do the same
thing
> -
> >downweight occipital pole etc and upweight the ventricle walls. I
guess
> >this would be slightly less accurate than doing it individually for
> each
> >input volume, but I would think you could downweight pretty big areas
> >without really detracting from the registration, so I would think
this
> >should be fine.
> >
> >
> >
> >
> >>3 - Following from 2, would there be any problems in doing a
straight
> >>image subtraction to identify the areas to be masked? It seems to me
> that
> >>this would be plagued by the same problems as in 2, but that it
would
> be a
> >>quicker way to go about it?
> >>
> >>
> >
> >I think this is answered by the previous point (??)
> >
> >
> >
> >>4 - The CBU page recommends smoothing the mask image (8mm in
> accordance
> >>with the SPM default). Would I also need to do this with FEAT? Would
I
> use
> >>5mm, as this is the FEAT default (or alternatively, whatever level I
> set
> >>it to)?
> >>
> >>
> >>
> >
> >I would think smoothing the mask image would be a good idea. However,
> the
> >smoothness here is different from the smoothness in Feat - here we
are
> >smoothing because of uncertainty in the location of the structures of
> >interest, not due to GRF theory etc. In this case, I would thing 8mm
> >smoothing of the mask image would be fine.
> >
> >
> >
> >>5 - As an aside, can someone tell me why the average epi template in
> SPM
> >>would be a poor choice as an intial highres? Does the fact that it's
> not
> >>the same brain as your subject introduce more problems than the
> advantage
> >>of having the added contrast?
> >>
> >>
> >>
> >
> >Usually going to an initial highres, you would want to be able to
> choose a
> >low number of degrees of freedom to get a really robust registration.
> If
> >you use a reference brain which is a different global shape to the
> input
> >brain, you will need a high number of degrees of freedom even to get
> close
> >to a good registration, so I would think it would not be particularly
> >advantageous to choose an averaged brain as an initial highres.
> >
> >Hope this is useful (and accurate!!)
> >
> >
> >T
> >
> >
> >
> >
> >
> >
> >
> >>Sorry if some of these questions seem a bit basic - still trying to
> get my
> >>head around all of this!
> >>Thanks heaps, I really appreciate your ongoing help!
> >>Alex
> >>
> >>
> >>
>

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