Hi guys -
1st thing - just to check. Presumably, when you did the initial
tractography, you entered str2diff.mat, not diff2str.mat during the
probtrack. This is important!!
Then in this case you are right. Your pathway will be in a different space
to your FA, so you have to move either the pathway, or the FA (or both).
I think there are arguments both ways. Andreas is right that you will have
less interpolation of the _data_ if you transform the fdt_paths; however,
you will lose resolution in the pathway.
Overall, I am not sure which is better, but my gut feeling would be to go
with transforming the FA to structural space.
If you want to do this, I think the settings in your initial email were
right..
Cheers
T
On Mon, 2 Jan 2006, Andreas Bartsch wrote:
> Not quite. If your patway is saved in structural space, I would generate the mask in that very space and transform just the mask into diffusion space (reference space would be diffusion, or the nodif-image). Check which image is in which space in fslview.
> Good luck-
> Cheers, Andreas
>
> ________________________________
>
> Von: FSL - FMRIB's Software Library im Auftrag von Kristen Lindgren
> Gesendet: Mo 02.01.2006 19:07
> An: [log in to unmask]
> Betreff: Re: [FSL] AW: [FSL] AW: [FSL] Calculating FA after probabilistic tractograp hy
>
>
>
> Thanks, Andreas. That's a good point. I didn't think of that. So in the
> ApplyXFM_gui, I should use str2diff.mat as the transformation matrix with
> anat as the reference volume and just enter fdt_paths as the input volume,
> right? Thanks for the input!
>
> Kristen
>
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library
> To: [log in to unmask]
> Sent: 1/2/2006 12:58 PM
> Subject: [FSL] AW: [FSL] AW: [FSL] Calculating FA after probabilistic
> tractograp hy
>
> Hi,
> why don't you want to proceed the other way around, i.e. transform the
> mask into diffusion space by the inverse of diff2str.mat)? If you
> transform the FA map, the interpolation may alter your FA values whereas
> getting a binary mask in diffusion space should be straight forward.
> Cheers-
> Andreas
>
> ________________________________
>
> Von: FSL - FMRIB's Software Library im Auftrag von Kristen Lindgren
> Gesendet: Mo 02.01.2006 17:58
> An: [log in to unmask]
> Betreff: Re: [FSL] AW: [FSL] Calculating FA after probabilistic
> tractograp hy
>
>
>
> Hello. I have a quick follow-up question to your instructions on how to
> calculate FA from probabilistic tractography. In previous e-mails, I
> was
> told to use the following commands to get this information:
>
> avwmaths_32R pathway -thr <threshold> -bin -mul dti_FA FAmask
> avwstats FAmask -M
>
> However, I just realized that my masks for probabilistic tractography
> (mode=twomasks_symm) were in anatomical space and not diffusion space;
> therefore, I had to apply the diff2str.mat transform during probtrack.
>
> Does this mean that I need to apply the diff2str.mat transform to dti_FA
> before using the above commands? If so, are these the selections I
> would
> make?
>
> Transformation matrix = diff2str.mat
> Input volume = dti_FA
> Reference Volume = anat (T1 image that was used for registration), based
> on
> existing volume
>
> Thanks for your help. Hope you had a great holiday!
>
> Kristen
>
--
-------------------------------------------------------------------------------
Tim Behrens
Centre for Functional MRI of the Brain
The John Radcliffe Hospital
Headley Way Oxford OX3 9DU
Oxford University
Work 01865 222782
Mobile 07980 884537
-------------------------------------------------------------------------------
|