Hi!

I have seen this: http://fsl.fmrib.ox.ac.uk/fsl/fsl-4.1.9/flirt/examples.html

To concatenate two transformations:

convert_xfm -omat AtoC.mat -concat BtoC.mat AtoB.mat


But still do not understand clearly because it is concatenating two linear matrices but as I have interpreted the paper, they concatenate one linear and on non-linear....I am lost...

Rosalia.




2014-10-07 15:08 GMT+02:00 Bryson Dietz <[log in to unmask]>:

Hey Rosalia,

1: Check out the following: http://fsl.fmrib.ox.ac.uk/fsl/fsl-4.1.9/fnirt/combining_warps.html

Although, I am assuming they performed an affine transformation on the bet-ed T1 to the MNI brain, and followed with a non-linear transform using the non-bet-ed T1 to the non-bet-ed MNI. So perhaps they meant to say that they concatenated the two linear-transforms (DWI -(6DOF)> T1 -(12DOF)> MNI).

This would be done using convert_xfm.

The command you could use to take a linear transform and non-linear transform is applywarp (example from web page example).

applywarp --ref=example_func --in=mask_in_standard_space --warp=highres2standard_warp_inv --postmat=highres2example_func.mat --out=mask_in_functional_space

2: Not sure about this point, perhaps someone else can comment.

Cheers,

Bryson

On Tue, Oct 7, 2014 at 8:43 AM, Rosalia Dacosta Aguayo <[log in to unmask]> wrote:

I have been reading a paper and I have been following its methodology step by step but there are a couple of issues I do not understand how to do and I would be very grateful if anyone of you could help me with them.

- First point it says:

"A diffusion-weighted image was rigidly transformed to T1 images and each T1 image was non linearly transformed to MNI space"

Well, I have done it, but then it follows:  The concatenation of these two transformations was used to transform FA images to MNI space?!! How??

- Second point it says:

....the deep white matter regions from the ICBM-DTI-81 white matter labels atlas were removed from the resulting mask?! How?? I figure that I have to binarize and set to 0 the labels from ICBM_DTI_81 atlas....but I am unsure about if this is correct....

Thank you in advance for all your kindness and your time.

Yours sincerely,

Rosalia.