<div dir="ltr">Hi Ahmad,<div><br></div><div>I notice your bvals file contains a single b=0 volume with an actual b-value of 5. MRtrix is currently only able to handle single-shell HARDI data, and blindly assumes that any non-zero b-value corresponds to one of the DW images (not ideal, I admit). I suspect all you need to do is set that first value in your bvals file to an actual zero...</div>
<div><br></div><div>Hope that helps.</div><div>Cheers,</div><div><br></div><div>Donald.</div><div> </div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 12 July 2013 22:08, A.S. KANAAN <span dir="ltr"><<a href="mailto:amadeus.kanaan@gmail.com" target="_blank">amadeus.kanaan@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Dr. Touriner, <br><br>I am currently running a Diffusion analysis on the <a href="https://www.dropbox.com/home/NKI_enhanced" target="_blank">NKI_enhanced</a> DWI sample using CSD for estimating the fODFs. <br>
This is the data acquisition protocol: <a href="http://fcon_1000.projects.nitrc.org/indi/pro/eNKI_RS_TRT/DIff_137.pdf" target="_blank">http://fcon_1000.projects.nitrc.org/indi/pro/eNKI_RS_TRT/DIff_137.pdf</a> . <br><br>In my process, I have used different maximum harmonic degrees (lmax 6,8,14) for estimating the response function and running CSD. The profile of the estimate response function looked normal in all three cases and in three different subjects (<a href="https://docs.google.com/file/d/0B836ny4-YXrTR2lMWEREazFGbTA/edit?usp=sharing" target="_blank">Example</a>), but the fODF estimates were problematic. In all three subjects (ages: 46,36,21) several voxels on only one side of the Corpus Collosum contained <a href="https://docs.google.com/file/d/0B836ny4-YXrTUUludXhsVzU1S00/edit?usp=sharing" target="_blank">weird fODFs representing crossing fibers.</a> As evident from the glyphs, tractography using both the deterministic and probabilistic algorithms (<a href="https://docs.google.com/file/d/0B836ny4-YXrTTEFablowQjRKQkk/edit?usp=sharing" target="_blank">SD_STREAM</a> and <a href="https://docs.google.com/file/d/0B836ny4-YXrTUkVyM1NsOG9Sbk0/edit?usp=sharing" target="_blank">SD_PROB</a>) did not generate anatomically sounds tracts. I tried using different radii of curvature and step lengths but the results were similar.<br>
<br>Here is my process...<br><br>Masks: A single fiber voxel mask (SF_mask.mif) and a White matter mask (WM_mask.mif) were generated from the FA map at thresholds of 0.7 and 0.2 respectively. <br>ERF: >> estimate_response -grad grad.txt -lmax 8 DWI_ED.nii SF_mask.mif ERF_lmax8.txt<br>
CSD: >> csdeconv -grad grad.txt -mask WM_mask.mif -seed WM_mask.mif -lmax 8 DWI_ed.nii ERF_lmax8.txt CSD_lmax8.mif<br><br> Looking at the RAW data, we noticed motion artifacts, some noise and straight lines that cross the brain on coronal sections (see link below). <br>
<br>Have you encountered this sort of a problem before for an acquisition with more than 100 diffusion encoding gradient directions? Is my process sound or do you think its a problem with the RAW data? <br><br>You can download the raw data as well as my results <a href="https://www.dropbox.com/sh/xbh77szqmlmrkoj/pAPjPDXcnd" target="_blank">here</a>. <br>
<br>Viele Grüße,<br>Ahmad Kanaan<br><span style="color:rgb(153,153,153)">__________________________________________________<br>
<span style="font-family:arial,helvetica,sans-serif"><span style="font-family:arial,helvetica,sans-serif"><span style="font-family:arial,helvetica,sans-serif">Max-Planck-Institut für Kognitions- und Neurowissenschaften<br>
Stephanstrasse 1a <br>
04103 Leipzig, Germany <br></span></span></span></span><br><br><span style="color:rgb(153,153,153)"></span>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><font color="#ff6600" size="1"><b>Dr Jacques-Donald Tournier<br></b></font><div><font color="#ff6600" size="1">Research Fellow</font></div><div><font size="1"><br>
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