Dear Rob,
thank you for your help,
I checked out the post and did it the way you suggested: first I transformed the flirt_trafo.mat via transformconvert to mtrix_trafo.txt and then I applied via mrtransform the transformation to my T1. When viewing the results everything looks good to me. But when I compare the inputs of the matrices (flirt_trafo.mat and mrtrix_trafo.txt) they slightly differ from each other. I guess although the matrices are not the same they do the same job in the end or are the results incorrect then?
Here the matrices:
mrtrix:
0.999928258585556 -0.00179227576370166 -0.0118482326670557 -2.34805592992597
0.00212362345003817 0.999605329869771 0.0280128311094757 -1.59255629536604
0.0117933496769622 -0.0280359811373596 0.999537370169424 -8.79857663443265
0 0 0 1fsl:
0.9999281434 -0.002123623205 -0.01179334855 38.4919582
0.001792275695 0.9996052859 -0.02803597963 24.78287935
0.0118482318 0.02801282988 0.9995373165 -51.18039925
0 0 0 1
Another question relates to the mrtransform command. While I have been reading some other post http://community.mrtrix.org/t/beginner-connectome-pipeline-updated/373/7 relating to this topic I was wondering about the -inverse option which all other user turned on? But why should I apply an inverse transform to my T1 in that case? Sorry but I am a bit confused right now, I guess I just misunderstood something easy, because I just applied the mrtrix-trafo without the -inverse option on and it works well.
Thank you I really appreciate your help!
Best
Max