Hi Salil,
As Matteo said, the mean diffusivity "_MD.nii.gz" file is what you are
looking for here.
Best,
Mike
On Wed, Feb 18, 2015 at 7:41 AM, Salil Soman <[log in to unmask]> wrote:
> Hi Mike,
>
> Thank you for your email. This looks great. Is there a way to compute the
> corresponding adc map (to help sort out the shine through)? I have a bunch
> of acquisitions where the isotropic images are distorted and am hoping to
> generate isotropic images from dti acquisitions that can benefit from
> eddy_correct while showing the same acute infarcts as the isotropic images,
> but at higher resolution / better spatial fidelity.
>
> Thanks!
>
> -Salil
>
>
> Date: Mon, 16 Feb 2015 11:32:41 -0500
> From: Michael Dwyer <[log in to unmask]>
> Subject: Re: Possible to output the trace image from FSL processing for
> DTI
>
>
> Hi Salil,
>
> The trace image is not used much quantitatively because it confounds T2
> effects with diffusion effects ("T2 shine-through"). That being said, it
> can still be very useful for picking out early ischemia with restricted
> diffusion.
>
> As far as I know, it is not a direct output from dtifit or other FSL
> tools.
> However, you can compute it yourself pretty easily. The trace image is just
> the geometric mean (not arithmetic mean) of the individual DWI-weighted
> direction images (without the b0 image included).
>
> trace = (bimg_1 * bimg_2 * bimg_3 * ... * bimg_n) ^ (1/n)
>
> Because there are a lot of images, you will likely run into floating point
> numerical issues if you try to calculate it like that, though. However, you
> can also calculate it as the exponential of the average of the logarithms
> of the individual images. You can do this using fslmaths as follows:
>
> First, put together all your non-b0 images. Assuming the b0s are at the
> beginning, you can do:
>
> > fslroi dwi_series dwi_nonb0 5 -1
>
> If they aren't at the beginning, you'll have to take them out more manually
> and splice things back together.
>
> Then take the logarithm:
>
> > fslmaths dwi_nonb0 -log dwi_nonb0_log
>
> Then average:
>
> > fslmaths dwi_non_b0_log -Tmean dwi_non_b0_log_mean
>
> Then exponentiate:
>
> > fslmaths dwi_non_b0_log_mean -exp trace
>
>
> You can do the last three steps in one line if you like:
>
> fslmaths dwi_nonb0 -log -Tmean -exp trace
>
>
> Hope this helps!
>
> Best,
> Mike
>
>
>
>
>
> On Sun, Feb 15, 2015 at 6:49 PM, Matteo Bastiani <
> [log in to unmask]> wrote:
>
> > Dear Salil,
> >
> > when you process your diffusion weighted dataset using the dtifit routine
> > implemented in FSL, you will get, amongst the other output files, one
> that
> > ends with “_MD.nii.gz”.
> > That is the mean diffusivity volume, which is what you are probably
> > looking for.
> >
> >
> > Cheers,
> > Matteo
> >
> >
> > > On 15 Feb 2015, at 19:43, Salil Soman <[log in to unmask]> wrote:
> > >
> > > Dear List Members,
> > >
> > > I was wondering if there is a way to output the trace image from a
> multi
> > direction DTI acquisitoin (e.g. 30 directions with single b value of 1000
> > with 5 b0 images)? To clarify, the trace image to which I am referring is
> > the diffusion weighted image that is routinely used in clinical practice,
> > generated automatically by the MRI scanner, for evaluating the presence
> of
> > strokes.
> > >
> > > Thank you for your time and consideration.
> > >
> > > Best wishes,
> > >
> > > Salil Soman, MD, MS
> >
> >
>
>
> --
> Michael G. Dwyer, Ph.D.
> Assistant Professor of Neurology and Biomedical Informatics
> Director of Technical Imaging Development
> Buffalo Neuroimaging Analysis Center
> University at Buffalo
> 100 High St. Buffalo NY 14203
> [log in to unmask]
> (716) 859-7065
>
--
Michael G. Dwyer, Ph.D.
Assistant Professor of Neurology and Biomedical Informatics
Director of Technical Imaging Development
Buffalo Neuroimaging Analysis Center
University at Buffalo
100 High St. Buffalo NY 14203
[log in to unmask]
(716) 859-7065
