Download details

Dorsal and median raphe nuclei template

This is only a simple document without a file.


The dorsal raphe (DR) and median raphe (MR) masks were delineated in subject PET space as described in "Beliveau V, Svarer C, Frokjaer VG, Knudsen GM, Greve DN, Fisher PM. Functional connectivity of the dorsal and median raphe nuclei at rest. Neuroimage. 2015 Aug 1;116:187-95", then normalized to the MNI152 space (ICBM) to produce a probability map across subjects.

To find the transformation to normal space, PET and MR were coregistered using bbregister and then the MR was registered to MNI152 using flirt+fnirt in FSL. The two transforms were then concatenated and the masks were transferred to MNI152 space using nearest neighbor interpolation; these masks are the ICBM152.fnirt. However, fnirt is sometimes imprecise to align brainstem correctly and an alternative procedure was proposed by "Napadow V, Dhond R, Kennedy D, Hui K, Makris N. Automated brainstem co-registration (ABC) for MRI. Neuroimage. 2006; 32:1113-1119".

Essentially, it is a first alignment with flirt followed by a second flirt alignment focusing on brainstem by using a weighing limited to that region. We have applied that method and got slightly different masks, although nothing drastic. In our opinion, this second (ICBM152.brainstem.flirt) method yields better results, but feel free to use whichever you like.

These masks have also been included in the latest version of the AAL atlas: 10.1016/j.neuroimage.2019.116189.


For questions related to the DR/MR masks, contact Vincent Beliveau.


Copyright © 2021, Neurobiology Research Unit, Rigshospitalet.


The following files are available for download below:

Size File Description
4 kB raphe_masks.zip Zipped file containing the DR/MR masks
Created 2021-03-04
Changed 2021-03-04
Size 0
Created by Peter Jensen
Changed by Peter Jensen
Downloads 15