Hi - it looks like things are nearly working. However, the alignment
between the two timepoints are not very good, probably because there
is very different bias field in the two images. I suspect that to get
a better registration you will need to try using FAST to remove the
bias before running SIENA. You can run FAST on brain-extracted
images, with the bias output turned on and lots of bias field
dilation. You can then apply this to the original data and hopefully
remove the bias before running SIENA.
Cheers.
On 24 Oct 2007, at 01:54, Buyean Lee wrote:
> Hi Steve,
>
> The six-digit reference number for this upload session is 754982.
>
> There are three compressed files.
>
> 1. whole SIENA output directory
> 2. MRI before treatment (meanC9726_s1_2.img)
> 3. MRI after treatment (meanC9726_s2_2.img)
>
> The two MRIs are the average images of the 9 Analyze format files
> which were converted from the DICOM files (I acquired the same MRI
> nine times in one session).
>
> Thanks a million for willing to take a look at the images.
>
> Buyean
>
> -----Original Message-----
> From: Steve Smith <[log in to unmask]>
> To: [log in to unmask]
> Sent: Mon, 15 Oct 2007 11:04 pm
> Subject: Re: [FSL] Using SIENA in monkey MRIs
>
> Hi,
>
> I would NOT realign the images before running SIENA/FAST etc. This
> is because doing this reduces the resolution of the image because
> of interpolation-related blurring. It's ok to use fslswapdim as
> that just switches the axes around without having to resample
> between voxels.
>
> Otherwise, yes, just send the whole SIENA output directory.
>
> Cheers.
>
> On 15 Oct 2007, at 17:48, Buyean Lee wrote:
>
> > Hi Steve,
> >
> > Would you let me know which files you want to see; there are
> three > kinds of MRIs?
> >
> > 1. Analyze file formats in the orientation of acquisition
> (because > the nose is too big, I couldn't use AC-PC alignment).
> > 2. Analyze file formats after AC-PC alignment; resliced images
> > 3. Nifti file formats after removing the neck and tissues outside
> > the skull (these are the files works best in SIENA).
> >
> > I think it might be informative if I can send you the whole >
> directory SIENA created so that you can see the report.
> > Please let me know if you want me to do it.
> >
> > Thank you,
> >
> > Buyean
> >
> > -----Original Message-----
> > From: Steve Smith <[log in to unmask]>
> > To: [log in to unmask]
> > Sent: Sun, 14 Oct 2007 3:35 am
> > Subject: Re: [FSL] Using SIENA in monkey MRIs
> >
> > Hi,
> >
> > Is the movement between the two timepoints after registration due
> > to atrophy effects of interest, or "real" misregistration?
> >
> > If you would like us to have a quick look, please upload the
> files > in a single compressed tarfile to
> > http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
> > and then email me the upload ID.
> >
> > Cheers.
> >
> >
> > On 11 Oct 2007, at 03:15, Buyean Lee wrote:
> >
> > > Hi Steve,
> > >
> > > Finally, I ran Siena with the monkey MRIs (it is just one >
> subject); > the siena_report.html looks much better in terms of >
> brain > extraction, coregistation, etc.
> > >
> > > This is what I did.
> > >
> > > 1. removed all tissues outside the skull and below the cerebellum.
> > > 2. modified the siena.sh in order to use separate BET option
> for > > two scans.
> > >
> > > Brain extraction is much better, but coregistration by FLIRT is
> > not > satisfactory.
> > > I can still see some movement in the overlap of the two >
> coregistred > MRIs.
> > >
> > > Is there any way for me to send these two MRIs to you so that
> you > > can take a look at them?
> > >
> > > I just don't know what else I can do to improve the BET and > >
> coregistration further.
> > >
> > > Thank you,
> > >
> > > Buyean
> > >
> > >
> > >
> > > -----Original Message-----
> > > From: Steve Smith <[log in to unmask]>
> > > To: [log in to unmask]
> > > Sent: Thu, 27 Sep 2007 1:20 am
> > > Subject: Re: [FSL] Using SIENA in monkey MRIs
> > >
> > > HI - you would also want to include a rasonable amount of the >
> outer > skull boundary that's near the brain boundary, as this gets
> > used in > SIENA.
> > >
> > > To choose a FOV in FSLView and then reduce the image by this:
> > > Click around and find the voxel coordinates (voxel not mm) that
> > > bound the region you want to keep.
> > > Find the xmin and xmax values, and calculate the xsize = xmax -
> xmin
> > > Same for y and z.
> > >
> > > Then run
> > >
> > > fslroi originalheadimage reducedimage xmin xsize ymin ysize
> zmin > zsize
> > >
> > > (do this for both timepoints separately)
> > >
> > > and feed the reducedimages into SIENA.
> > >
> > >
> > > Cheers.
> > >
> > > On 26 Sep 2007, at 23:52, Buyean Lee wrote:
> > >
> > > > Hi Steve,
> > > >
> > > > "Alternatively, you could work out how to reduce the field-of-
> > > view > to just include the brain of each time point before
> feeding > > the > output of that into SIENA. You would use FSLView
> on each > > image to > work out the field-of-view and then use
> fslroi to reduce > > the FOV of > the image."
> > > >
> > > > I created a whole brain mask for the animal brain using FSLView.
> > > >
> > > > But, it is not easy to understand how to use fslroi.
> > > >
> > > > fslroi <input> <ouput> <xmin> <xsize> <ymin> ...
> > > >
> > > > I just don't know how to determine these parameters and when
> I > am > > supposed to use the mask file in fslroi.
> > > >
> > > > Would you kindly let me know how to reduce the field-of-view
> to > > > include the brain?
> > > >
> > > >
> > > > Thank you,
> > > >
> > > > Buyean
> > > > > >
> ----------------------------------------------------------------------
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> > > Stephen M. Smith, Professor of Biomedical Engineering
> > > Associate Director, Oxford University FMRIB Centre
> > >
> > > FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> > > +44 (0) 1865 222726 (fax 222717)
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> ----------------------------------------------------------------------
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> > Stephen M. Smith, Professor of Biomedical Engineering
> > Associate Director, Oxford University FMRIB Centre
> >
> > FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> > +44 (0) 1865 222726 (fax 222717)
> > [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> >
> ----------------------------------------------------------------------
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> ----------------------------------------------------------------------
> -----
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ----------------------------------------------------------------------
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> Check Out the new free AIM(R) Mail -- Unlimited storage and
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------------------------------------------------------------------------
---
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
------------------------------------------------------------------------
---
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