Dear Alain,

thank you again for your answer. It has been very helpful. However, I still have a doubt. If the output of the query is the percentage of each field in the atlas that overlap in my cluster, should not be the sum of all percentages 100%?

In contrast, I've got the following output:

GM Amygdala_centromedial group L:10.8723
GM Amygdala_laterobasal group L:62.4839
GM Amygdala_superficial group L:40.7047
GM Hippocampus cornu ammonis L:13.6064
GM Hippocampus entorhinal cortex L:6.38563
GM Hippocampus dentate gyrus L:2.22074
GM Hippocampus hippocampal-amygdaloid transition area L:2.69946
GM Hippocampus subiculum L:5.8085
WM Cingulum L:0.18617
WM Corticospinal tract L:0.164893
WM Optic radiation L:0.757977
WM Uncinate fascicle L:0.223404

If I sum them all, it exceed 100. I assume that the probability of each field it is the probability that such field has to belong to the given cluster, rather than the percentage of the cluster taken up for that field.

Then, I still would like to know if there is a way to know the real percentage of the cluster belonging to a given field

Many thanks,

Maria



On Tue, Nov 3, 2015 at 11:45 AM, Alain Imaging <[log in to unmask]> wrote:

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.



--
Maria Serra Blasco
Institut d'Investigació Biomèdica de l'Hospital de la Santa Creu i Sant Pau, IIB-Sant Pau
Av. Sant Antoni Ma. Claret, 167
Tlf: +34 93 5537836
08025 Barcelona- Spain

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