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Hi Suraj,

FLIRT calculates linear transformations (global translations,
rotations, and scalings), which are stored in plain-text .mat files.

FNIRT calculates non-linear transformations, which potentially contain
a different amount of displacement at each voxel. So FNIRT
transfornations are stored as image files, and there is no way to
convert them to a .mat file.

But you can combine linear and non-linear transformations with the
convertwarp command - use the --premat and --postmat options to pass
the .mat files.

Cheers,

Paul

On 08/01/2019, Suraj Thyagaraj <[log in to unmask]> wrote:
> Hi everyone,
>
> I have certain ROIs that are in the MNI_1mm space that I would like to bring
> to the subject specific DWI space to perform tractography. Using FNIRT I
> have registered the MNI space (A) with the subject structural space (B) as
> follows:
>
> fnirt --ref=$SUBJECT_DIR/T1.nii.gz --in=$MNI_DIR/MNI152_T1_1mm.nii.gz
> --aff=$SUBJECT_DIR/affine.mat --cout=$SUBJECT_DIR/MNI152_FNIRTed.nii.gz
>
> In addition I have done linear registration between the subject structural
> space (B) and the subject DWI space (C) as follows:
>
> {FSLDIR}/fsl/bin/flirt -in $SUBJECT_DIR/T1.nii.gz -ref
> $SUBJECT_DIR/DWI_b0.nii.gz -out $SUBJECT_DIR/T1_in_DWI.nii.gz -omat
> $SUBJECT_DIR/T1_in_DWI.mat' -bins 256 -cost corratio -searchrx -90 90
> -searchry -90 90 -searchrz -90 90 -dof 12  -interp trilinear
>
> I would like to combine these two transformations to create a transformation
> between the MNI space (A) and the subject DWI space (C).
>
> I saw that both convert_xfm and convertwarp can be used to combine
> transformation but I'm faced with these issues:
>
> i) convert_xfm requires two .mat files like so: convert_xfm -omat
> <outmat_AtoC> -concat <mat_BtoC> <mat_AtoB> , but for the FNIRT operation, I
> only get an output .nii.gz file. Is there a way to get the transformation
> file as a .mat file from FNIRT? How can I use convert_xfm given my previous
> steps?
>
> ii) convertwarp uses two warp.nii.gz file but the transformation file from
> FLIRT is a .mat file. How can I use convertwarp given my previous steps?
>
> Thanks for any help!
>
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