<div dir="ltr">Dear Donald & Team,<div><br></div><div>Let me introduce myself. My name is Alistair Perry and I am a post-graduate student at UNSW. Additionally Michael Breakspear at QIMR is my co-supervisor, so I will be using their pipeline, and I will meet you guys later in May.</div>
<div><br></div><div>I know this has been covered in previous posts, but this is an amalgamation of issues.</div><div><br></div><div>First, we have collected data in par/rec format from a 3T phillips scanner (b/vals = 1000, 31 directional). As obviously the gradient coordinates are not in mrtrix space and no DICOM format available, I had to flip the X-coordinates to achieve the desired result. I have attached the formatted encoding file. Could you confirm this is the correct for MRtrix?</div>
<div><br></div><div>However, in doing so, and running csdeconv, I receive a number of error messages: <b>csdeconv failed to converge</b> (I guess around +100 times). I have checked the resulting CSD orientation plot and everything appears to be ok, as does the resulting probalistic fiber tracks. There doesn't appear to be any voxels blacked out, although we are using elderly subjects with obvious cortical atrophy. <br>
<br>Suprisingly, when testing different iterations of the encoding file (i.e flipping Y or Z coordinates) this error did not appear. Could you explain why this is so? Is there a frequency of messages where it becomes a concern?</div>
<div><br></div><div>Thanks,</div><div><br></div><div>Alistair Perry</div></div>