[Mristudio-users] Skull Strip in ROIEditor

[susumu mori]

Hi Jeff,

There are two ways to do it. One is to use the ROI tools and the other is to
use the "skull-strip tool" (the right-most button in the "Tool" section).
The former is more manual and the latter is more automated.

When you use the automated skull-strip button, you have an access to the
overwhelming number of parameters. We haven't tested this function
thoroughly. This is a type of region growing tool with which you can control
the edge detection and smoothness of the boundary. This is written by Yue
Li.

Yue, I wonder if you could write a brief summary about which parameter does
what.

The manual way is the more old-fashioned ROI-based masking. Please do the
following to get some idea.

1) Load JHU-MNI-SS-FA from the "Sample atlas" section.
2) Also open b0 and DWI within the same window, so that you have FA/b0/DWI
all in one window. Don't open images with "ss", which are already skull
stripped.
3) If you look at b0 or DWI, you can find that skull has very low intensity.
So they are the best one to remove skull. Let's use b0 for this example.
4) Bring the b0 to the active image displayed.
5) Click "Seed Region Growing" in the "Tool" section
6) set the low threshold to 40, choose 3D, and click the center of the brain
7) you can see the brain is nicely defined by red color.
8) Click "Add" button in "Selection" section
9) The brain boundary is now registered as "object 1".
10) Go to "+.-,/,x" button and combine the FA and Object 1 by "masking".
Click OK.
11) You can get a new FA map masked by Object 1.
12) If you want manual touch up, you can modify the Object 1 using the "Pen"
tool in "Selection" followed by "Add" or "Remove" button

Hope this will help.

Susumu
On Mon, Jun 7, 2010 at 5:14 PM, Jeff Sadino <jsadino.queens at gmail.com>wrote:

> Aloha DTI experts,
>
> I wanted to create a skull stripped image in ROIEditor.  I remember reading instructions on it a couple months ago where it said to use intensity thresholding and growing.  It was a bit more manual.  I see the following message sent on May 20.  I wanted to do it the more manual way though.  I looked all over the website, but can not find those instructions again.  If anyone remembers what I'm referring to, could they please send me the link to where those instructions disappeared to?
>
>
> Thank you very much,
> Jeff Sadino
>
> Open ROIEditor
> Click folder icon (under File on top toolbar); choose b0 (change parameters
> according to your image dimensions/type)
> 1.     Scroll down; under TOOL, click button with oval icon (Skull
>
>
> Stripping; last button on right)
> 1.     Choose ŒSkull strip the current archive image only.¹; click OK
> 2.     Change Segment Downsample (1,2,or 3) to 1; click OK
> Under IMAGE, click folder icon (Load Image File); choose FA.dat (same image
>
>
> parameters as b0)
> Under ROI, click icon with +/-/x/÷ signs (Operation; 1st button)
> 1.     In left box choose SkullStrippedMaskByte_<filename>.b0
> 2.     In center pull-down menu choose Multiplication
> 3.     In right box choose FA.dat; click OK
>
>
> Under IMAGE, click disc icon (Save Image File)
> 1.     In left box choose SkullStripped_<filename>.b0, click arrow, click OK
> 2.     Save as <filename>.b0ss
> 3.     Repeat save, choose Multiply_
> SkullStrippedMaskByte_<filename>.b0_FA.dat, click arrow, click OK
>
>
> 4.     Save as <filename.fass
>
> Hope this helps,
>
> Julie
>
> Julie E. McEntee, MA, CCRP
> Senior Research Program Coordinator
> Department of Psychiatry- Neuroimaging
> Johns Hopkins University School of Medicine
>
>
> 600 N. Wolfe St./Phipps 300
> Baltimore, MD 21287
> Phone: 410-502-0468
> Fax: 410-614-3676
>
>
> On 5/20/10 3:39 PM, "Naama Barnea-Goraly" <naamab at stanford.edu <http://lists.mristudio.org/mailman/listinfo/mristudio-users>> wrote:
>
>
> >*
> *>* Could anyone send out a step by step process for skull stripping in
> *>* ROIeditor? (perhaps using a B0 image?).
> *>*
> *>* Thanks,
> *>*
> *>* Naama
>
> *>*
> *>*
> *>*
> *>* Naama Barnea-Goraly M.D.
> *>* Instructor
> *>* Center for Interdisciplinary Brain Sciences Research
> *>* Stanford University Division of Child and Adolescent Psychiatry
>
> *>* 401 Quarry Rd. MC 5795
> *>* Stanford University School of Medicine
> *>* Stanford, CA  94305-5795
> *>* Phone: (650) 736-1874, fax: (650) 724-4794
> *>*
> *>*
>
> *>* CONFIDENTIALITY NOTICE:  This e-mail communication and any attachments
> *>* may contain confidential information for the use of the designated
> *>* recipients named above.  If you are not the intended recipient, you
>
> *>* are hereby notified that you have received this communication in error
> *>* and that any review, disclosure, dissemination, distribution or
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