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Hi, Another trick might be to use: fslmeants -i maskfile -m maskfile --showall | head -3 > mask_coordinate.txt This will give you instead of 0's and 1's the voxel coordinates of the mask in a 3-row format with X as first row, y as second row ... Maybe this is a fast intermediate step for what you want to achieve. good luck, wolf On 10/14/2009 09:04 AM, Jasper Luyendijk wrote: > Hi, > > If I'm not mistaken the 'fsl2ascii' command under fslutils in the list of tools (FSL-website) converts images (nii) to text files. > > Jasper > > > -----Original Message----- > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Rolf Heckemann > Sent: woensdag 14 oktober 2009 8:58 > To: [log in to unmask] > Subject: Re: [FSL] how to read bet binary mask > > Ying > > As far as I'm aware, you cannot convert NIfTI to ASCII with FSL, but > an external utility will do it. Try (X)MedCon > <http://xmedcon.sourceforge.net/> > > Rolf > > > On Tue, Oct 13, 2009 at 10:36:21PM +0100, Ying Chen wrote: > >> Hello, >> >> Bet2 -m option generates binary brain mask, with 0 outside the brain and 1 >> inside the brain. The output brain mask is in .nii.gz format. My questions >> is how I can read it as a text file which has a bunch of zeros and ones. Do >> I need to convert .nii.gz format to another kind of format to be able to >> read the text version of the brain mask? >> >> Thanks a lot in advance, >> Ying >> >