[Mristudio-users] Skull Strip in ROIEditor

[Jeff Sadino]

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
*>* copying of it or its contents is prohibited.  If you have received
*>* this communication in error, please notify Stanford Medical Center
*>* immediately by telephone at (650) 725-5722 and destroy all copies of
*>* this communication and any attachments.  Thank you.
*
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