Hi Jennifer, if you find Brian script a bit too fancy for you, I believe Michael Scheel has replied early this morning with another very straightforward and appropriate way to do exactly what you want to do... Cheers, Gwenaelle --- En date de : Mar 17.3.09, Bramen, Jennifer E. <[log in to unmask]> a écrit : > De: Bramen, Jennifer E. <[log in to unmask]> > Objet: Re: [FSL] Using atlas regions as a mask > À: [log in to unmask] > Date: Mardi 17 Mars 2009, 19h01 > Yes, I already know about the mask, which contains all roi > in it. Each ROI is identified by making it a different > interger value and color. What I do not know is if there is > a way to break apart this mask into several. individual ROI > rather than one mask with ALL roi. Is there a command that > will do this? Create seperate files for each region? Or do I > have to trace over each one and save a new mask? > > Thank you. > > Best regards, > > > Jennifer Bramen, Ph.D. > Assistant Research Neuroscientist > UCLA Center for Cognitive Neuroscience > Developmental Cognitive Neuroimaging > David Geffen School of Medicine at UCLA > 635 Charles Young Drive South > Los Angeles, CA 90095-7332 > Phone: (310)267-5116 > Fax: (310)525-0865 > Email: [log in to unmask] > Campus Mail Code 176919 > > ________________________________________ > From: FSL - FMRIB's Software Library > [[log in to unmask]] On Behalf Of Nestor, Liam (Contractor) > [[log in to unmask]] > Sent: 17 March 2009 09:53 > To: [log in to unmask] > Subject: Re: [FSL] Using atlas regions as a mask > > If you go to: > > fmri/atlases/HarvardOxford/HarvardOxford-combo-maxprob-thr25-2mm > > You will be able to see predefined rois masks which have > already been set up in FSL. There are not actually labelled, > so you will have to overlay them in FSL view to establish > which roi masks correspond to which region of the brain. > > I am assuming that you want to use these for functional > data, in which case case you input these rois (one at a > time) when you perform your higher level FEAT analyses. Here > you are confining the thresholding to a particular region > (e.g., left ACC). FEAT will ignore all voxel outside the roi > mask. In post-stats, you input the roi mask where is says > "pre-threshold masking". > > Perhaps there are other methods you can use, but perhaps > give this one a go. > > Liam. > > > ******************************************* > Liam Nestor, Ph.D > Office C8-523 > Laboratory for Molecular Neuroimaging > Semel Institute for Neuroscience and Human Behavior > 760 Westwood Plaza > Los Angeles 90024 > Tel: 310-206-0655 > E-mail: [log in to unmask] > ******************************************* > ________________________________________ > From: FSL - FMRIB's Software Library > [[log in to unmask]] On Behalf Of Teena Moody > [[log in to unmask]] > Sent: Tuesday, March 17, 2009 9:40 AM > To: [log in to unmask] > Subject: Re: [FSL] Using atlas regions as a mask > > Jen, > Ashley, Jesse and I have some ROIs already made for several > regions > from the MNI 25 and 50% atlases. We probably have slightly > different > methods, I will try to send you notes that Ashley sent me. > I forward > an old email if i can find it. > Teena > On Mar 16, 2009, at 2:07 PM, Jennifer Bramen wrote: > > > Dear FSL List > > > > I would like to use individual regions of interest > from one of the > > free atlases. However, the > > atlases are composed of multiple regions and I do not > know how to > > create a separate mask > > for an individual region. Is there a command I can > use? > > > > Thanks > > > > jen > > Teena Moody > [log in to unmask] > > > Semel Institute at UCLA > > 760 Westwood Blvd. Suite B8-169 > > Los Angeles, CA 90095 > > (310) 794-9360 lab > > (310)503-5630 cell > > [log in to unmask] > > IMPORTANT WARNING: This email (and any attachments) is > only intended for the use of the person or entity to which > it is addressed, and may contain information that is > privileged and confidential. You, the recipient, are > obligated to maintain it in a safe, secure and confidential > manner. Unauthorized redisclosure or failure to maintain > confidentiality may subject you to federal and state > penalties. If you are not the intended recipient, please > immediately notify us by return email, and delete this > message from your computer. > > IMPORTANT WARNING: This email (and any attachments) is > only intended for the use of the person or entity to which > it is addressed, and may contain information that is > privileged and confidential. You, the recipient, are > obligated to maintain it in a safe, secure and confidential > manner. Unauthorized redisclosure or failure to maintain > confidentiality may subject you to federal and state > penalties. If you are not the intended recipient, please > immediately notify us by return email, and delete this > message from your computer.