Hi Nina,
That's not quite right.
You need to do:
cat myvoxelcoords.txt | img2stdcoord -img mysrcimage.nii.gz -xfm myimage2std.mat -std $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz -vox - > standardspace.txt
The input (myvoxelcoords.txt) and output (standardspace.txt) need to be space separated values, not comma separated values, and you need to specific the image that the coordinates relate to as well as the standard space image and the flirt matrix from the registration of the image to standard space. If the image is already in standard space then you can skip the "-xfm myimage2std.mat" part.
I hope this helps.
All the best,
Mark
> On 9 Mar 2017, at 04:20, Nina de Lacy <[log in to unmask]> wrote:
>
> Hi there:
>
> I have a flat file with (essentially) a list x,y,z coordinates in voxel space. I would like to convert them to mm (MNI space). The man page seems to suggest I can do this with a flat file using img2stdcoord (I think)
>
> Something like this work?
>
> cat coordfile.txt | img2stdcoord -src myvoxelcoords.csv -dest standardspace.csv
>
> Thanks
> Nina
>
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