Dear K,

Thanks very much for your reply. I have looked at the original FA volumes visually, and can't see any indication of slice to slice signal variations in most of these participants. I did have one subject with that issue which completely threw off warping, and I have previously dropped them from the analysis.The severity of this banding/ringing does vary from volume to volume in all_FA, but is present in most of the volumes to some extent.

At this point I'm wondering what other options there are to salvage this data - perhaps it is simply not suitable for warping to the template? Smoothing the eroded images (after tbss_1_preproc) makes the banding less obvious, but I am hesitant to smooth given how this may affect analyses.

it is conceivable also that it is an effect of relatively large voxels in the original volume being resampled to much finer voxels. I think I would need to see the data to be able to say anything with certainty. Could you please upload (http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi) the original FA image together with the warp-file so that I can look at them? When you do you will be given a reference number that you can email me "off" the mailbase.

Jesper

On Tue, Sep 28, 2010 at 7:53 AM, Jesper Andersson <[log in to unmask]> wrote:

Dear K,

I am looking at some DTI data in TBSS. I followed tbss_2_reg and tbss_3_postreg scripts to transform the data to MNI space. After looking at all_FA.nii I noticed some significant banding distortion in a number of the images, though the alignment it self looks to be ok.
Any idea what could be causing these problems? They are present in a lot of the participants volumes and I'm worried they are significantly impacting results (though perhaps the skeleton minimizes their contribution somewhat).
Note I was aligning to the standard template. I've attached an example image to this message

I have noticed these in the past as well, and in those cases they have been caused by slice-wise signal variations that fnirt then rotated away from the plane and into these diagonal bands. Can I ask you to first of all go back to your original image and see if you can identify them there? They are much less conspicuous when running parallel with the planes.

Jesper