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Dear Melissa,
I fully agree with Eugenio's view and recommendation.
Basically, there has been different historical traditions in regard to thalamic segmentations. You can find attached Figure 19.2 from Mai & Forutan (2012) which shows differences just between some authors in their thalamic nuclei delineation. In other words, different authors have had different conceptions regarding the classification and delineations of thalamic nuclei. For instance, differences are quite notable in some ventral and lateral nuclei, with different territories depending on the classification. And that can apply to other nuclei depending on the classifications you compare.
When we started working on our thalamic nuclei atlas (Iglesias et al., 2018), we decided to based our clasification/segmentation on the work done by Jones (2012), which presents quite extraordinary detail in its characterization of the thalamic nuclei. We combined high resolution ex vivo MRI and histology, so the neuroanatomist (Ricardo Insausti) was able to delineate with the best possible precision the different nuclei while having next to him Jones's book to check any detail. So, our atlas and companion segmentation derives from Jones's previous work and it is related to his view regarding thalamic nuclei organization (see Jones, 1998). So, it does not have the same nuclei and the same delineation than other classifications, such as the ones from Morel.
In my view, the mentioned "validation" studies from the same first author are comparing things that are conceptually different and are subjected to circularity. As Eugenio pointed out, if you compare different thalamic segmentations to the Morel atlas and our atlas of the thalamus is based on Jones (not Morel) and other ones are based on Morel, which ones are going to look more similar to Morel? But in any case, again these are different conceptual classifications, so if any comparison is done, they need to be done with all the caution.
So, as Eugenio mentioned, at this point you can see the advantages or disadvantages or using one or other thalamic nuclei segmentation and go with any of them. There is a consensus among researchers in the neuroscience field regarding the need of bringing a common delineation/classification unifying different coneptual approaches and nomenclatures in thalamic nuclei segmentation. There are plans for having at some point a gathering to work on that. But as far as I know, these are just plans.
Hope this can be of any help.
Best,
Kp.
References:
Jones, E.G., 2012. The Thalamus. Springer Science & Business Media.
Jones, E.G., 1998. Viewpoint: The core and matrix of thalamic organization. Neuroscience. 85 (2): 331– 345
Mai, J.K., Forutan, F., 2012. Thalamus. In: The Human Nervous System, Third Edition. Elsevier, pp. 618–677.
- Pedro "Kepa" Paz-Alonso, Ph.D. Group leader, BCBL Ikerbasque Research Professor Ikerbasque Researcher profile Ikerbasque: https://secure-web.cisco.com/176cf5yMCrjsKE7mehNbZbSpwntD7QRGfnXp99NCFtOeY1f...
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From: "Iglesias Gonzalez, Juan E.,PHD" JIGLESIASGONZALEZ@mgh.harvard.edu To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Cc: "Pedro Paz-Alonso" p.pazalonso@bcbl.eu Sent: Friday, October 17, 2025 8:16:59 PM Subject: RE: Validation of the thalamic nuclei segmentation
Dear Melissa,
I am CCing the senior author Dr. Paz-Alonso so he can also chime in (I wish I could also CC the neuroanatomist that made the annotations, but, sadly, he passed away last year).
THOMAS is great but the underlying atlases used Morel as basis for manual segmentation so it is expected that they agree better with the atlas… and, even then, if you look at the Dice scores in the paper, there are plenty of nuclei where FS is higher. I actually find the experiments on AD staging / classification more compelling.
Our atlas has the advanrage of working with any MRI contrast “out of the box”, and is pretty good at snapping to the boundaries of the mediodorsal and posterior nuclei (pulvinar), especially if you provide images with good contrast. But if you have images that match the contrast of THOMAS well, then by all means exploit that agreement and use THOMAS!
Just my 2 cents 😉
Kind regards,
/Eugenio
From: Melissa Thalhammer melissa.thalhammer@tum.de Sent: Friday, October 17, 2025 3:12 AM To: Freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Validation of the thalamic nuclei segmentation
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Dear FreeSurfers,
I read that criticism about the thalamic nuclei segmentation based on T1-images was raised ( DOI: [ https://secure-web.cisco.com/1eJxYpKwA2ZQnNHzMzqolRLQbHC3La8ApnjzLguJLU7IC-g... | 10.1016/j.neuroimage.2022.119340 ] and DOI: [ https://secure-web.cisco.com/1Xt62fHdzFAPsCkjEP3euJAJBHslctTFBLGq6CU_IfHiqFp... | 10.1162/imag_a_00166 ] ) as overlaps with the Morel stereotactic atlas were not always satisfying. However, I was wondering whether the segmentations with the Morel atlas (registered to MNI space) of individual thalami can be considered a proper validation since individual variation of thalamic nuclei sizes are not taken into account and the atlas is not probabilistic.
Can someone elaborate on this criticism?
Thank you, Melissa
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