[Mristudio-users] cut operation

[Woo, John]

Susumu and Hangyi -

Thank you for both your responses.  I'll have to think about them a
little more deeply.

All my ROIs were drawn in the axial plane, so I'm not sure if Hangyi's
explanation applies.

However, Susumu's response is interesting, and certainly seems to be a
plausible explanation why there sometimes may be an asymmetry between
cut(ROI1,ROI2) and cut(ROI2,ROI1).  The effect of the seed point and its
relation to the fiber hadn't occurred to me.

At any rate, the differences are very minor (usually no difference, or
at most one pixel).  I was only interested in getting a more "exact"
understanding of the process.

- John.

-----Original Message-----
From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of
support at mristudio.org
Sent: Thursday, August 14, 2008 11:43 AM
To: DTI Studio, ROI Editor,Landmarker Questions/Support
Subject: Re: [Mristudio-users] cut operation

Hi John,

when a fiber passing through a voxel, there are usually 2 intersection
points,
one is for entering, one is for exiting. if what you said "ROI
intersects the
fiber in two points" means this situation, the result of cut operation
depends
on the 2D-slice direction where the ROI was drawn. take a 2D as a
example:

  |  A /  |
------/-------
  |  /    |
  | /     |
B /       |
-/-------------
/ |       |
  |       |

if you drawing the ROI in horizontal slicing direction, the "cut
operation" will
result point A. on the other hand, if the ROI was drawn in vertical
slicing
direction, the result is B.

when you dealing with digital grid, this happens all the time. this is
something
related to digitizing error.

hangyi






> Hi John,
>
>
>
> That is a good question. I need Hangyi's answer for more detail, but
my
> guess is the following points are related to this issue;
>
>
>
> 1) As you know, in DtiStudio fiber tracking is completed in the
beginning
> from the center of all pixels with FA values above the threshold.
>
> 2) If we draw two ROIs and select fibers that penetrate the both ROIs,
there
> are two classes of fibers;
>
> a) The seed pixels are within the two ROIs
>
> b) The seed pixels are outside the two ROIs
>
> 3) If there are fibers that penetrate one ROI twice, the (a) and (b)
class
> may pick up different points for the crossing. Also, it may become
sensitive
> to the order of ROI drawing. Of course, this becomes an issue only
when we
> use the "CUT" operation.
>
>
>
> Hangyi, do you think this is really the case?
>
>
>
> I hope these differences cause only minor problems, but if not please
let us
> know.
>
>
>
> Susumu
>
>
>
>   _____
>
> From: mristudio-users-bounces at mristudio.org
> [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Woo, John
> Sent: Wednesday, August 13, 2008 2:52 PM
> To: mristudio-users at mristudio.org
> Subject: [Mristudio-users] cut operation
>
>
>
> Hi, I've been trying to understand the "cut" operation of defining the
> voxels between two ROIs.
>
>
>
> Each fiber intersects both ROIs.  I can see that
"nSelectFiberStartPoint"
> and "nSelectFiberEndPoint" determine the indices of the cut points.
If the
> fiber intersects each ROI in exactly one point, I can confirm that
these are
> precisely the points.
>
>
>
> But if say ROI 1 intersects the fiber in two points, it is not
entirely
> clear to me which point is chosen.  It seems that sometimes the first
is
> chosen, sometimes the second.
>
>
>
> Interestingly, in an attempt to elucidate the process further, I tried
> swapping the two ROIs of the cut operation (by altering the ".map"
file).
> The resulting fiber depends on the order of the ROIs.  That is,
> cut(ROI1,ROI2) does not always equal cut(ROI2,ROI1), although they are
> almost identical.
>
>
>
> Thanks to anyone who can help.
>
>
>
> -John.
>
>
>
>
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