Dear all

I would like to create new ROIs of bilateral hypothalamus (not in the standard atlas tools of CONN) 

according to a research paper
https://doi.org/10.1007/s11695-019-03822...
and the hypothalamic MRI atlas by Baroncini
LH (x ± 6, y − 9, z − 10 plus 2 mm sphere)
MH (x ± 4, y − 2, z − 12 plus 2 mm sphere)
The coordinates of LH and MH are in standard space (MNI space).


1. can I automatically define this in CONN, or must I pass via e.g. MRICron

2. how to I get it into CONN

3. can I also use these ROIs for 2nd level analyses ROI-ROI ?

THANKS !!

Sven

Hi Sven,

In the Setup.ROIs tab, you may select "ROI tools" and "Create new ROIs from MNI coordinates" to create and import those ROIs from their MNI coordinates and sphere sizes. Then simply propagate those changes to the second-level results tab (i.e. run each step selecting the "do not overwrite" option, so that only these new ROIs are processed) and you should be able to use them as seeds in any of your analyses. 

Hope this helps
Alfonso

Originally posted by Sven HALLER:

I recommend also overlaying the ROI on your normalized functional data to ensure that it fits where you expect it to.

Hello Sven -

Since you have the 3D coordinates of your ROI, you can also use the Wake Forest Pick Atlas. I created ROIs for the pre SMA and SMA using this.

best,

Alan Francis

Dear Alfonso

thanks again ! This worked !

Originally posted by Alfonso Nieto-Castanon:

I did - thanks for the advise

Dear Alan

thanks for the suggestion

I was able to do it as recommended by Alfonso. But thanks a lot for the suggestion !

Sven