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Hi Again, Yes, you can script up the calls that ApplyXFM makes to fslcreatehd and flirt. Just look at the terminal window that you start the GUI from. It shows you these commands (separated by a semicolon). These are the only two commands you need to run to do the same thing, and in fslcreatehd you just need to modify the number of voxels and voxel size, which are easily identified from this output or from the help for fslcreatehd. All the best, Mark On 30 Oct 2008, at 06:51, Anthony Ang wrote: > Hi Mark, > > Is it possible to script ApplyXFM at the command line rather than > using its GUI ? > I have 60 images so if they can be resliced to 2x2x2 mm voxel > resolution as a batch in a script file, this will be much easier > than entering the values in the GUI screen one image by one image. > > The command line equivalent for ApplyXFM appears rather complicated: > fslcreatehd .......... > > Thanks for your help and sorry for bothering you so many times. > > Best regards > Anthony > > On Tue, Oct 28, 2008 at 8:51 PM, Mark Jenkinson > <[log in to unmask]> wrote: > Hi, > > To make the 2mm reference image you can use ApplyXFM and set > the output size to be based on Voxel Dimensions. I made it have > 91x93x88 voxels, each of 2x2x2mm for your data, in order to have > the same FOV. > > All the best, > Mark > > > >