Hi Mark,
thank you for the precision, very useful.

For voxel intersection, I am trying with -mas command or with image binarisation, as you have indicated;

I have another two naive queries about atlases; (sorry for the juvenile attitude but I have started with fsl by some weeks)

1) the 4th dimension in the 4D atlas is the probability related to some region?

2) in my fsl atlas folder (Juelich as example) I have this files:

-rw-r--r-- 1 root 208031 giu 11 2010 Juelich-maxprob-thr0-1mm.nii.gz
-rw-r--r-- 1 root   38212 giu 11 2010 Juelich-maxprob-thr0-2mm.nii.gz
-rw-r--r-- 1 root 162746 giu 11 2010 Juelich-maxprob-thr25-1mm.nii.gz
-rw-r--r-- 1 root   28807 giu 11 2010 Juelich-maxprob-thr25-2mm.nii.gz
-rw-r--r-- 1 root 126708 giu 11 2010 Juelich-maxprob-thr50-1mm.nii.gz
-rw-r--r-- 1 root   20790 giu 11 2010 Juelich-maxprob-thr50-2mm.nii.gz
-rw-r--r-- 1 root 3572376 set 11 2013 Juelich-prob-1mm.nii.gz
-rw-r--r-- 1 root 581414 set 11 2013 Juelich-prob-2mm.nii.gz

What's the difference between maxprob file and prob one?

Best
AAV

The label numbers do start from zero in the xml file and from zero as volume numbers in the 4D probability files, but they start from one in the maxprob label files (as in the latter case zero is reserved for the background). This is always something that is inconsistent between 4D probability versions and 3D label versions and you just have to keep track of that.

As for finding the voxels of the intersection, I think it would be much better to form the volumetric intersection mask using fslmaths (the -mas option will do what you want, or just multiple two binarised images) and then you can extract the coordinates from this intersection mask.

From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Alberto <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Monday, 28 December 2015 08:20
To: "[log in to unmask]" <[log in to unmask]>
Subject: Re: [FSL] atlases' coordinate

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