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Dear FSL experts,

I have subjects with two dti 4D adquisitions (dti1 and dti2 with 31 sequences). 

I have a question about how to split my 4D dti1 data into 3D in order to get a single 3D nifti volume containing the volume of DWI for b0 value....so, I should co-register volumes within dti1 to b0 value as the reference volume.

I have been looking at applyxfm 4D usage with Flirt in the mailing list ...and I think it could be the best option for my objective

[rosalia@UB17-336-161116099027 ~]$ applyxfm4D
Usage: applyxfm4D <input volume> <ref volume> <output volume> <transformation matrix file/[dir]> [-singlematrix/-fourdigit/-userprefix <prefix>]]
[rosalia@UB17-336-161116099027 ~]$ 

But I am unsure about how to fix this with my subjects....

Any example of suggestion about this issue?

Thanks in advance,

Rosalia.


2012/4/21 Rosalia Dacosta <[log in to unmask]>
Hi Mat,

I  have to separate the b0 value from my dti adquisition in order to get a single 3D nifti volume containing the volume of DWI for the 0 b-value....I know I have to use flirt, but I don't know how to manage to calculate and apply a transformation to each of the volumes of 4D DTI sequences of my subjects.... :(

I have been searching at the fsl mailing list but I had not been lucky. 

Please, could you help me with this question?

Thank you very much.

Rosalia.