I have a tensor image generated by DR TAMAS. I want to transform this tensor image to a scalar image template (T1 or T2).
What command should I use?
I tried used DTIREG:
DTIREG --moving_tensor tensor.nii --fixed_scalars T1_template.nii
But it was not working.
Should I use the tensor to generate a FA image, and then use ANTS to transform the FA to the T1_template.nii, and then use DR TAMAS to read the transformation from ANTS and apply it to the tensor?
Can DR TAMAS read the transformation files from ANTS?
Or there is a more direct way to do it?
Thanks a lot!
There are several ways in DRTAMAS to co-register the DTI and T1/T2 template. To address your question, it would be helpful to know if your ultimate goal is to co-register the templates or specifically bring the DTI template into the T1/T2 template space?
I have created a T1/T2 template using ANTS, and DTI template using DRTAMAS.
Yes, I want to bring the DTI template into the T1/T2 template space.
Using nonlinear method to bring the DTI template into the T1/T2 template space.
DRTAMAS is again for tensor operations only. So what I suggest is to ComputeTRMAp (Trace or in otherwords MD), out of the tensor template. Then use ANTS to register this on to your T1/T2 template.
Then you can combine the affine/diffeomorphic transformations coming out of ANTS and Apply the Transformation to DRTAMAS tensor with "ApplyTransformationToTensor"
hope this helps.
How to combine "the affine/diffeomorphic transformations coming out of ANTS " to format that is compatible with "ApplyTransformationToTensor'
CombineTransformations didn't recognize the transformation files from ANTS.
Sorry should have given more details.
First you need to convert the affine_transform.mat into a txt with:
ConvertTransformFile 3 affine_transform.mat affine_transform.txt
Then you can use CombineTransformations:
CombineTransformationsWithOutputName -out combined_deffield.nii.gz -trans affine.txt diffeo.nii.gz
Then you can apply it:
ApplyTransformationToTensor average_template_diffeo_6.nii combined_deffield.nii.gz average_template_diffeo_6_tranformed.nii FS your_T2_template.nii
hope this helps.
Thanks. That's helpful