That is correct.
I would use the image that is most similar
in FOV to the diffusion image. It probably won’t matter, but if there is
a really big difference sometimes FLIRT will make a mistake (though this is
less likely if you use only 6 degrees of freedom).
Peace,
Matt.
From:
Sent: Wednesday, February 03, 2010
10:13 PM
To: [log in to unmask]
Subject: Re: [FSL] Is probtrackx
results binned in standard space by default?
Thank
you！ I think I've got the point. So I just have to
provide the seed region in standard space, and use the transformation
parameters derived from fdt registration. The probtrackx will give out the
results in standard space. Is it right?
I
've got another question :). I transformed the
data from dicom to fsl nifti by dcm2nii, which produced 3 results(reoriented
& cropped images) for each 3d-t1 volume. I suppose the one with a co-
prefix is the one I should use. The image produced by a windows version of
dcm2nii was cropped about right below the cerebellum,
while the dcm2nii in linux cropped the image at the level of mouth.
I compared the two images with the dti image, and found the first one more
alike.
Here is the question. In registration, do we have to choose images alike (or,
do we have to crop the t1 images to match the other images)? I think
the registration process would perform
according to absolute coordinate, but not the revelant
position between
images. Is it right?
Thanks
Yu
2010/2/4
Saad Jbabdi <[log in to unmask]>
Hi
Yu
The results of probtrackx are binned in seed space. If you want your results to
be binned in standard space, you can transform your seed into standard space
and then feed the transformed seed and the transformation from standard to
diffusion space to probtrackx.
Cheers,
Saad.
On 3 Feb 2010, at 13:27, huangpy py wrote:
> Dear experts
>
> It is said in the fsl tutorial that results from probtrackx can be binned
in any available space, but I haven't seen any options for output in the gui
(it has options for transforming the seed region). If I have to warp the
results into standard space manually, which command should I use? In
the FDT-registration, does it just produce the transformation .mat file?
>
> thanks
>
> Yu
--
Saad Jbabdi
JR Hospital,
(+44)1865-222466 (fax 717)
www.fmrib.ox.ac.uk/~saad