Dear all,<div><br></div><div>This is a follow up of my previous email. After checking several factors, it seems overall the "flags" file works, but the realignment has shifted the slices. Therefore, after realignment good slices (previously bad) are tagged as bad slices. An example of what happens can be found here:</div>
<div><a href="http://img69.imageshack.us/img69/4112/artifactsandrealigment.jpg">http://img69.imageshack.us/img69/4112/artifactsandrealigment.jpg</a></div><div><br></div><div>In order to understand better the issue, realignment parameters can tell something. For example the volume on the figure has these realignment values:</div>
<div><br></div><div><div> -- AIR-Matrix for: Scan10.REC - 9 --</div><div> Path-Name: C:\Scan10.REC --</div><div> AIR 4x4 matrix</div><div> 1.0000 0.0025 0.0022 -0.5762</div><div> -0.0025 1.0000 0.0006 -0.5945</div>
<div> -0.0022 -0.0006 1.0000 0.9537</div><div> 0.0000 0.0000 0.0000 1.0000</div></div><div><br></div><div>Which of these paramters is rotation and which is shift? Are the values in millimeters or in voxels?</div>
<div><br></div><div><br></div><div>Your comments on the issue are much appreciated.</div><div><br></div><div><br></div><div>Dorian</div><div><br></div><div><br><div class="gmail_quote">
2013/3/22 Dorian P. <span dir="ltr"><<a href="mailto:alb.net@gmail.com" target="_blank">alb.net@gmail.com</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi everybody,<div><br></div><div>I am using the "flags" file to label bad volumes in 3 loaded datasets. After labeling bad volumes, I save the dataset in raw format (all 3 datasets become a single .dat file). I load back the raw format, which now is only 1 long line of volumes, and the flagged volumes do not correspond. As a result, corrupted slices are still visible in FA maps, compromising the study.</div>
<div><br></div><div>I had the impression that the "flags" file can be reloaded on the same dataset, even when saved as raw, but now I am confused. Can you please explain how does a flags work when loaded with a concatenated long dataset? I can send you the par/rec files and the .dat file if necessary.</div>
<div><br></div><div>Thank you and enjoy the weekend.</div><div><br></div><div>Dorian</div><div>Thomas Jefferson University</div>
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