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FSL  August 2009

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Subject:

Re: transforming coordinates from standard to subject space

From:

Mark Jenkinson <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Mon, 10 Aug 2009 22:01:31 +0100

Content-Type:

text/plain

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text/plain (119 lines)

Hi,

I'm surprised that a coordinate within the brain will be transformed  
outside
the FOV.  Have you checked coordinates that are not near the edge of the
brain?

Your flirt call is fine if you want to do that instead.

All the best,
	Mark


On 10 Aug 2009, at 20:27, Mengfei Huang wrote:

> Hi Mark,
>
> I just tried that and ended up with coordinates that fell off of my  
> highres brain (y coordinate). Is this a reasonable problem to  
> encounter due to inaccuracies in the transformation matrix, or would  
> this indicate that something has gone wrong?
>
> If it's the former, I'll go back and just transform the original  
> mask into subject space first before picking the peak voxel. i  
> believe that would be:
>  flirt -in [mask in standard space] -ref reg/standard -applyxfm - 
> init standard2highres.mat -out [mask in subject space] correct?
>
> thanks!
> Mengfei
>
> On Mon, Aug 10, 2009 at 7:41 PM, Mark Jenkinson  
> <[log in to unmask]> wrote:
> Hi,
>
> 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 text.
> 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,
>        Mark
>
>
>
> 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!
> Mengfei
>
> On Mon, Aug 10, 2009 at 6:08 PM, Mark Jenkinson  
> <[log in to unmask]> wrote:
> Hi,
>
> Just use the tool std2imgcoord.
>
> All the best,
>       Mark
>
>
>
> 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  
> syntax?
>
> I've seen it done for nii.gz images but not specific coordinates
>
> Many thanks!
> Mengfei
>
>
>
>
> -- 
> Mengfei Huang
> Fulbright Scholar (UK) 2008-2009
> MSc Neuroscience
> Oxford University
> BS Biological Sciences
> Stanford University
>
>
>
>
> -- 
> Mengfei Huang
> Fulbright Scholar (UK) 2008-2009
> MSc Neuroscience
> Oxford University
> BS Biological Sciences
> Stanford University
>

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