[Mrtrix-discussion] ignoreslices AND coregister

["Samuel Gröschel"]

Hi Donald,

With some delay I am back in your wonderful MRtrix and have again some beginners questions.

1. I would like to discard some slices with artefacts from my analysis. The command "dwi2tensor" makes this possible with the option "-ignoreslices" as I can see in the documentation. First part of the question is how many slices can I discard in order for the following analyses to run smoothly? Second part is the error message I get when I want to discard more than one slice. E.g. when entering

dwi2tensor dwi.mif dt.mif -ignoreslices 0 36 -ignoreslices 1 6,8,57

I get the message "dwi2tensor: multiple instances of option "ignoreslices" are not allowed"

What did I do wrong?

2. The other question I have is about realigning the anatomical image (3dflash) to the diffusion images. This would be important in order to define seed and target regions more accurately and also to overlay tracks on the anatomical image. Unfortunately the anatomical image is not in the same spatial dimension (subject probably moved between the scans). As you said, in theory it should be possible to coregister the anatomical image to the b0 image. B0 can be obtained by the following command:

mrconvert dwi.mif -coord 3 0 b0.img

First thing I realised is that when transforming the ".mif"-images to the analyse-format (img/hdr) using "mrconvert" the mif and img images appear in a slightly different position on "mrview". Therefore the tracks can only be overlayed correctly onto mif-files.

I tried coregistering the anat.img to b0.img in SPM. Unfortunately both images had not the same voxel positions in z-dimension using the display function in SPM. Could it be due to the fact that in the b0-image brain stem and inferior part of cerebellum is cut off? I also tried with FLIRT (fsl) but without success so far. What would you recommend? Do you have experience with coregistering using flirt in that case?

Thanks for your help and best regards,

Samuel