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
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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