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If you are going to dilate the BAs, then you should select all of them and perform the dilation. Then, you can use imcalc to select the ones of interest. You can't dilate only 1 BA at a time otherwise they will bleed into other areas, especially with a dilation of 3. For the posterior cingulate cortex in the aal atlas: Cingulum_Post_L Cingulum_Post_R Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. On Thu, Apr 30, 2015 at 6:09 PM, Mahsa Alizade shalchy <[log in to unmask] > wrote: > Dear Donald > > Thank you so very much, I now know how to tackle my DMN problem. > I would be more than grateful if you could help me with my last question. > I would like to make an ROI of posterior cingulate cortex but I could not > find the exact label in pickAtlas list of labels so I tried using BA 29 and > 30 instead. > Since the BAs are really thin (considering WFU pickAtlas) shouldn't I use > up to 3 dilations? > > Many thanks in advance, > Mahsa > > > > > On Thursday, April 30, 2015 1:31 AM, "MCLAREN, Donald" < > [log in to unmask]> wrote: > > > You'll need to use a clustering program to write out the different DMN > regions to use each one as a separate structural ROI. > > I wouldn't use dilation for BAs as you are only selecting a few and you'd > dilate into surrounding BAs. > > Best Regards, Donald McLaren > ================= > D.G. McLaren, Ph.D. > Research Fellow, Department of Neurology, Massachusetts General Hospital > and > Harvard Medical School > Postdoctoral Research Fellow, GRECC, Bedford VA > Website: http://www.martinos.org/~mclaren > Office: (773) 406-2464 > ===================== > This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED > HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is > intended only for the use of the individual or entity named above. If the > reader of the e-mail is not the intended recipient or the employee or agent > responsible for delivering it to the intended recipient, you are hereby > notified that you are in possession of confidential and privileged > information. Any unauthorized use, disclosure, copying or the taking of any > action in reliance on the contents of this information is strictly > prohibited and may be unlawful. If you have received this e-mail > unintentionally, please immediately notify the sender via telephone at > (773) > 406-2464 or email. > > On Wed, Apr 29, 2015 at 2:03 AM, Mahsa Alizade shalchy < > [log in to unmask]> wrote: > > Dear Donlad > > Thank you so much for taking the time to answer. > After obtaining DMN (i.e. using ICA) how could I have each region > (pcc,mpfc...) as a structural ROI? > Secondly, using BAs what dilation should I use ? > I highly appreciate your help. > > Best Regards, > Mahsa > > > > On Tuesday, April 28, 2015 8:18 PM, "MCLAREN, Donald" < > [log in to unmask]> wrote: > > > If you want DMN regions, then you need to pick a paper and replicate their > methods. The DMN doesn't occupy entire BA or entire gyri/sulci, so often a > course parcellation on that scale isn't optimal. > > The RSN from the FSL group are available online and you can use them. > > If you want spheres around the hubs of the DMN, see Yeo et al. 2011 (Table > 5). > Thomas Yeo, B. T., Krienen, F. M., Sepulcre, J., Sabuncu, M. R., Lashkari, > D., Hollinshead, M., et al. (2011). The organization of the human cerebral > cortex estimated by intrinsic functional connectivity. Journal of > Neurophysiology, 106(3), 1125-1165. doi:10.1152/jn.00338.2011 > > Best Regards, Donald McLaren > ================= > D.G. McLaren, Ph.D. > Research Fellow, Department of Neurology, Massachusetts General Hospital > and > Harvard Medical School > Postdoctoral Research Fellow, GRECC, Bedford VA > Website: http://www.martinos.org/~mclaren > Office: (773) 406-2464 > ===================== > This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED > HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is > intended only for the use of the individual or entity named above. If the > reader of the e-mail is not the intended recipient or the employee or agent > responsible for delivering it to the intended recipient, you are hereby > notified that you are in possession of confidential and privileged > information. Any unauthorized use, disclosure, copying or the taking of any > action in reliance on the contents of this information is strictly > prohibited and may be unlawful. If you have received this e-mail > unintentionally, please immediately notify the sender via telephone at > (773) > 406-2464 or email. > > On Mon, Apr 27, 2015 at 1:24 AM, Mahsa Alizade shalchy < > [log in to unmask]> wrote: > > Dear Experts, > Hi > > I would like to show each component of DMN (i.e. PCC, MPFC,...) with a > separate structural ROI, using pickAtlas. However, I'm not sure which > regions to choose from pickatlas menu. > Since, different papers introduced different regions as DMN (i.e one the > of the papers selected 14 BAs for presenting DMN and the other study > selected only 5 BAs,....) I'm really confused. > Secondly, I would like to make ROIs of Posterior cingulate cortex, Medial > prefrontal cortex, Left inferior temporal cortex and right inferior > temporal cortex but could not find the same labels. Could I use Posterior > cingulate, Medial frontal gyrus and Inferior parietal lobule instead? > > Many thanks in advance, > Mahsa > > > > > > > >