Print

Print
Hi,

We have a tool specifically for this: img2stdcoord
It will work with either matrices (for linear registration) or warp fields (for non-linear registration).

If you have used non-linear registration then you must use the highres2standard_warp file, but you do not need to use the matrix file (as that is already encoded in the warp file).  The applywarp command you've used will only apply the linear transformation that is used to initialise the non-linear transformation.  It will look approximately right, but should not be as accurate as the non-linear result.

For more details on img2stdcoord see:
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT/UserGuide?highlight=%28img2stdcoord%29#img2stdcoord

All the best,
Mark



On 6 Aug 2018, at 05:16, SUBSCRIBE FSL Robin Cash <[log in to unmask]> wrote:

Hi,
I am trying to convert a specific set of voxel coordinates from native to standard space. I have tried everything I can think of, including multiplication by the highres2standard matrix. Could you offer any suggestions on how I could do this?

As additional background, I used non-linear registration during preprocessing. I found that the highres2standard matrix sufficed for converting the anatomical image from native to standard space. I assumed it would require a warp file but it doesn't seem to. Does that seem correct? The following code works (without a --warp input):

applywarp --ref=/usr/local/fsl/data/standard/MNI152_T1_2mm_brain.nii.gz --in=/$path/anat/anat_native.nii.gz --premat=$path/Prestats.feat/reg/highres2standard.mat --out=$path/anat_standard.nii.gz;

Many thanks,
Robin

########################################################################

To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1


To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1