That's not quite right.
The syntax is:
std2imgcoord -img reg/highres -std reg/standard -xfm reg/
highres2standard.mat -vox coordfile
where coordfile contains your input coordinates (in standard space) as
The output goes to the screen.
To capture it in a file just end the line with: > outputfile.txt
as the ">" operator in Unix directs the output (of any command) into
the following file.
You are right that you give it the highres2standard.mat
transformation, which it internally
inverts, to convert coordinates from standard to highres space.
All the best,
On 10 Aug 2009, at 19:34, Mengfei Huang wrote:
> Hi Mark,
> so just to double check the syntax would be:
> std2imgcoord -img <text file containing voxel coordinates> -std reg/
> standard -xfm <subject's hires2standard.mat> <output coordinate file
> in subject space> -vox (to output coordinates in voxels)
> Is this correct? So even though you're using the hires2standard
> matrix, it converts from standard to hires?
> Thank you!
> On Mon, Aug 10, 2009 at 6:08 PM, Mark Jenkinson
> <[log in to unmask]> wrote:
> Just use the tool std2imgcoord.
> All the best,
> On 10 Aug 2009, at 18:04, Mengfei H wrote:
> Dear FSL,
> Is it possible to use FLIRT to transform voxel coordinates (x,y,z)
> from standard
> space back into subject space? If so, what would be appropriate
> I've seen it done for nii.gz images but not specific coordinates
> Many thanks!
> Mengfei Huang
> Fulbright Scholar (UK) 2008-2009
> MSc Neuroscience
> Oxford University
> BS Biological Sciences
> Stanford University