[Mristudio-users] Flags file mismatch when reloaded

[Dorian P.]

Dear all,

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:
http://img69.imageshack.us/img69/4112/artifactsandrealigment.jpg

In order to understand better the issue, realignment parameters can tell
something. For example the volume on the figure has these realignment
values:

  -- AIR-Matrix for: Scan10.REC - 9 --
          Path-Name: C:\Scan10.REC --
 AIR 4x4 matrix
   1.0000    0.0025    0.0022   -0.5762
  -0.0025    1.0000    0.0006   -0.5945
  -0.0022   -0.0006    1.0000    0.9537
   0.0000    0.0000    0.0000    1.0000

Which of these paramters is rotation and which is shift? Are the values
in millimeters or in voxels?


Your comments on the issue are much appreciated.


Dorian


2013/3/22 Dorian P. <alb.net at gmail.com>

> Hi everybody,
>
> 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.
>
> 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.
>
> Thank you and enjoy the weekend.
>
> Dorian
> Thomas Jefferson University
>
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