[Mristudio-users] about effect of masking

[Jim Li]

Hi Susumu,

Thanks a lot for your information. I tried the skull-stripping of ROIEditor
using the default setting. The result is not bad, but I hope to add/remove
some areas manually on top of the outcoming mask file to define a better
mask. Also I hope to better understand the default parameters in the
skull-stripping algorithm so I can tailor them to my need. I wish there's an
instruction manual for ROIEditor that can tell me all of these...

Cheers,

Jim

-----------------------------------------

Hi Jim,

When you do tensor calculation, you want to mask out the areas outside
the brain. The easiest way is to use the threshold value to mask out
the noise floor. This approach however leaves a lot of extra-brain
tissues. RoiEditor (and many other programs) offers much more tools to
define the brain as a binary map and remove other tissues using tools
such as region growing and skull-strip tools. If you have any binary
masking generated by another program you can load such a file through
this function.

Susumu

------Original Message------
From: Jim Li
Sender: mristudio-users-bounces at mristudio.org
<http://lists.mristudio.org/mailman/listinfo/mristudio-users>
To: DTI Studio, ROI Editor, Landmarker Questions/Support
ReplyTo: DTI Studio, ROI Editor,	Landmarker Questions/Support
Subject: [Mristudio-users] about effect of masking
Sent: Dec 5, 2008 17:57

Hi all,   Can anybody give me a hint?   In the  DTIstudio software I
clicked the "Tensor, Color map, etc" button in the "Calculation"
section of the "DtiMap" tab. Then, from the pop-out window called
"DTI-Map Options", I saw a choice called "Select a mask-image". Under
what situation should we use that choice? Should it be a default
choice when the brain has some lesions, given that the lesional area
can be at about the same level as the background noise level and thus
can be easily wiped out even if we choose a low background noise level
from which to create a mask-image?     Thanks a lot,   Jim
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