Hi Javier,<div><br></div><div>A funny-looking response function is typically a consequence of a suboptimal 'single-fibre' mask. In your case, your response is actually not too bad - certainly good enough to get decent results - but yes, it can be improved. </div>
<div><br></div><div>The issue is that the automated procedure used to derive the 'single-fibre' mask is admittedly a little rough and ready, so you really need to check that it's OK before proceeding to the next stage. The main thing to look out for is that all voxels included in the mask are placed in actual white matter, in regions that (are thought to) contain single fibre orientations. It's often necessary to edit this mask to exclude noisy, high FA voxels at the edge of the brain, etc. You should also modify some of the commands you use, which will help to produce a more robust mask. I typically use:</div>
<div><br></div><div><span style="font-family:Tahoma;font-size:13px">$ </span><span style="font-family:Tahoma;font-size:13px;font-weight:bold">average</span><span style="font-family:Tahoma;font-size:13px"> img_dwi.nii -axis 3 - | threshold - - | median3D - - | median3D - img_dwi_mask.mif</span><br style="font-family:Tahoma;font-size:13px">
<br>to get the whole-brain mask, and:<br><br><span style="font-family:Tahoma;font-size:13px;font-weight:bold">$ erode</span><span style="font-family:Tahoma;font-size:13px"> img_mask.mif -npass 3 - | erode - - | mrmult img_mask_fa.mif - - | threshold - -abs 0.7 img_mask_sf.mif</span><br style="font-family:Tahoma;font-size:13px">
<br>to get the single-fibre mask. Note that these are the commands recommended in the documentation for the latest release. I will then have a brief look at the mask overlaid on the FA map just to check there aren't too many voxels in non-WM regions, and edit if required - it's fine to leave a few bad voxels in there, no need for it to be perfect. After that, the response function should be fine.</div>
<div><br></div><div>Hope that helps,</div><div><br></div><div>Donald.</div><div><br></div><div><font face="Tahoma"><span style="font-size:13px"><br></span></font></div><div><font face="Tahoma"><span style="font-size:13px"><br>
</span></font><div class="gmail_quote">On 25 July 2012 15:40, Mr Javier Urriola Yaksic <span dir="ltr"><<a href="mailto:javier.urriolayaksic@uq.net.au" target="_blank">javier.urriolayaksic@uq.net.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div style="direction:ltr;font-size:10pt;font-family:Tahoma">Dear Donald,<br>
<br>
I'm new using MRtrix. Therefore, I'm following the online manual as close as possible in order to understand the whole process to get reliable results.<br>
While reading the manual I noticed that my CSD response image (attached in this mail) looks slightly different compared to the on-line image of the manual. The axial plane is larger than the z-axis as expected, yet in the centre of the response function rendering
is folded slightly outwards (see images). <br>
So far, I haven't figure out what is the cause of this and if it would affect my results?<br>
Thanks!<br>
Regards,<br>
<br>
Javier Urriola Y.<br>
<br>
<br>
Code used:<br>
$ <span style="font-weight:bold">mrconvert</span> img_dwi.nii -coord 3 0 - | threshold - - | median3D - - | median3D - img_dwi_mask.mif<br>
<br>
$ <span style="font-weight:bold">dwi2tensor</span> img_dwi.nii -grad z_iy_xb_dir.txt - | mrmult - img_mask.mif img_dtmask.mif<br>
<br>
$ <span style="font-weight:bold">tensor2FA</span> img_dtmask.mif - | mrmult - img_mask.mif img_mask_fa.mif<br>
<br>
$ <span style="font-weight:bold">tensor2vector</span> img_dtmask.mif - | mrmult - img_mask_fa.mif img_mask_ev.mif<br>
<br>
<span style="font-weight:bold">erode</span> img_mask.mif - | erode - - | mrmult img_mask_fa.mif - - | threshold - -abs 0.7 img_mask_sf.mif<br>
<br>
<span style="font-weight:bold">estimate_response</span> img_dwi.nii img_mask_sf.mif -lmax 6 img_mask_response.txt -grad z_iy_xb_dir.txt<br>
<br>
<span style="font-weight:bold">disp_profile</span> -response img_mask_response.txt<br>
<br>
<br>
<br>
<br>
</div>
</div>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br>Jacques-Donald Tournier (PhD)<br>Brain Research Institute, Melbourne, Australia<br>Tel: +61 (0)3 9035 7033<br>
</div>