Yes it might be right. Thanks Matthew.
Also I have note that the numeration of the intensities (the labels) start from zero in the .xml file and from 1 in the fslview. This implies that when you mask you don't have to insert the number of .xml atlas but the number you see in the fslview intensity.

About x,y,z : I have created a txt file with all volumes of Juelich 0-1 mm and only frontal volumes of Harvard-Oxford (std & lateral) 0-1 mm. It is a file with 3 colums (x,y,z) and millions rows (all coordinates number). Manage this file is not easy (ms excel 2011 and matlab dont allow it). My haim is to select coordinates repetition beetween the atlases represented in this file in order to have only unic x,y,z by atlases union.

Thank you in advance if you have some hints about how to handle this big file.

Best
AAV
From: Matthew Webster
Sent: ‎27/‎12/‎2015 15:15
To: [log in to unmask]
Subject: Re: [FSL] atlases' coordinate

Hello,
  These are probably the voxel co-ordinates for the 2mm version of the atlas - hence why the values double for the higher resolution atlas.

Kind Regards
Matthew

> Dear fsl experts,
>
> I am comparing coordinates from different atlases and what I have found is that the x,y,z of an atlas.xml file are different of the same atlas open with fslview. Why is this?
>
> I make an example from HarvardOxford-Lateralized: in the .xml file, the Left Frontal Pole has x=63 y=86 z=49 , instead the 0-1mm.nii.gz of the same region file has x =126 y=172 z=98
>
> Thank you in advance
> Best
> AAV