Hi Mark,
is this revision (below) now incorporated into a general FSL download?
Take care, Darren
----- Original Message -----
From: "Mark Jenkinson" <[log in to unmask]>
To: <[log in to unmask]>
Sent: Monday, April 28, 2003 8:20 AM
Subject: Re: [FSL] img2talcoord problem
> Hi,
>
> Yes, it appears that this is a bug in img2talcoord (and also in
> tal2imgcoord) - sorry.
> An easy fix for any existing output is to take the y coordinate,
> multiply by -1 and subtract 32 from the result.
> That is: Y_correct = -1*Y - 32
>
> This should give the same values as in the output from Feat (via cluster)
> which is correct.
>
> This was a result of not removing some of the medx y-coordinate
> conventions correctly (the default behaviour without -flirt, which uses
> medx conventions, is correct).
>
> I've made new linux, macosx and alpha binaries for img2talcoord and
> tal2imgcoord
> that can be downloaded from
> http://www.fmrib.ox.ac.uk/~mark/files/img2talcoord/
>
> If anyone needs an irix or sun binary, let me know and I'll organise
> something.
> Sorry for the trouble,
> Mark
>
>
>
> Zrinka Bilusic wrote:
>
> > Hello,
> > as I was working on some things (possibly another question later on)
> > with talairach coordinates and I have run into a problem. I tried to
> > use img2talcoord to get tal coordinates for a list of voxels in the
> > original space. here is the command I have used...
> >
> > img2talcoord -tal standard -img example_func -xfm
> > example_func2standard.mat -vox -flirt original_coords.txt >
> > mni_coords.txt
> >
> > I have run this within the reg/ folder, and original_coords.txt is a
> > modified Imax_zstat1.txt file from the same analysis. I just wanted to
> > confirm that I will get the same coordinates as are reported in the
> > feat report (in cluster_zstat1_tal.html, and listed in
> > Imax_zstat1_tal.txt). But I do not get the same numbers! Here are just
> > a few coordinates from the list...
> >
> > original coordinates (voxels)
> > 30 5 3
> > 35 8 0
> > 30 6 1
> > 27 4 5
> >
> > corresponding tal coordinates from Imax_zstat1_tal.txt (result of feat
> > analysis)
> > 6.95 -92.4 19.1
> > -9.38 -85.7 2.32
> > 6.96 -91.3 8.14
> > 16.8 -93.7 29.8
> >
> > and here are the coordinates output by img2talcoord
> > 6.95002 60.3709 19.1
> > -9.37855 53.7371 2.3233
> > 6.96059 59.3127 8.13768
> > 16.839 61.7015 29.7874
> >
> > As you can see, the y coordinates are way off. Why? I have
> > doublechecked all my files: input functionals are in the same
> > orientation (Posterior on top) as the standard file (mni standard);
> > there is nothing out of the ordinary in the header files for the
> > functional as well as the high res used in the registration. And the
> > registration results are very good. Have I just used img2talcoord
> > incorrectly, or is there something else that I am missing?
> >
> > Thank you!
> >
> > Zrinka Bilusic-Vezmar
> > UCLA Brain Mapping
> > 660 Charles Young Drive South
> > Los Angeles, CA 90095
> >
> > 310-794-5060
> > [log in to unmask]
> > www.brainmapping.org
>
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