Hi - try 'convertwarp'…this allows you to concatenate linear and non-linear transformations.
Best,
Ricarda
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Ricarda Menke, PhD
Oxford Centre for Functional MRI of the Brain (FMRIB)
Nuffield Department of Clinical Neurosciences
University of Oxford
John Radcliffe Hospital
phone: 0044 1865 222 738
On 7 Oct 2014, at 14:33, Rosalia Dacosta Aguayo <[log in to unmask]> wrote:
> 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.
>
>
