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Dear Maria


you can do a query on the atlas using this command


atlasquery -a "Juelich Histological Atlas" -m your_binarised_cluster.nii


This will give you the percentage of each field in the atlas that overlap with your cluster


Best


Alain



De : FSL - FMRIB's Software Library <[log in to unmask]> de la part de Maria Serra <[log in to unmask]>
Envoyé : mardi 3 novembre 2015 10:57
À : [log in to unmask]
Objet : Re: [FSL] results from randomise (shape analysis)
 
Dear Alain,

thank you for answering. I used FIRST indeed, so as you pointed out it is easy to identify the structure as a whole. However, what I would like to know, in the case of the amygdala for example, which percentage of the cluster belongs to laterobasal subregion, which one to centromedial and which one to superficial subregion (according to Juelich histological atlas).

Thank you in advance,

Maria Serra

On Mon, Nov 2, 2015 at 2:17 PM, Alain Imaging <[log in to unmask]> wrote:

Dear Maria, 

you could take a look at atlasquery, using the appropriate atlas (I guess in your case it would be the Harvard-Oxford Subcortical strucutral atlas) and a binary image of your cluster.

Note also that since the FIRST segmentation is based on a model that is in the standard space, I am not sure that you need an atlas query to confirm that your cluster is in the left amygdala, since it is the left amygdala by definition, if you segmented it using FIRST.

Best

Alain
De : FSL - FMRIB's Software Library <[log in to unmask]> de la part de Maria Serra <[log in to unmask]>
Envoyé : lundi 2 novembre 2015 12:36
À : [log in to unmask]
Objet : [FSL] results from randomise (shape analysis)
 
Dear FSL users, 

I would like to know if there is a way to know the percentaje of a brain region included in a given cluster. That is to say, if my results show shape differences in a cluster located in the amygdala (i.e. which percentaje belongs to lateral amygdala).

Thanks in advance,

--
Maria


P Abans d'imprimir aquest correu electrònic pensa bé si és necessari fer-ho.



--
Maria


P Abans d'imprimir aquest correu electrònic pensa bé si és necessari fer-ho.