Hi,

I think the quality here will depend on how well colin_tlrc_1x1x1.nii.gz actually matches the Talairach space.  You have only done a linear registration, so this might not be that good, as the mapping between the spaces is not quite that simple.

Have you looked at the thalamic nucleus mask on top of this image (prior to registration)?  If that looks good and the registration of that image to the MNI looks good then things should be OK.  So I suspect that one or other of these things is at fault.

Alternatively, you might like to look at transformations that other people have investigated for mapping Talairach to MNI coordinates.  For instance:

http://www.brainmap.org/icbm2tal/

or

http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach

though I'm sure there are others too.

These have been fairly carefully looked at, so should probably work well.

All the best,

            Mark

Recently, and following much appreciated input, I used the below call

in FLIRT to calculate a Talairach to MNI transform; the initial step

in transferring a thalamic nucleus mask created in Talairach space to

MNI space

 

flirt -ref $FSLDIR/data/standard/MNI152_T1_1mm_brain -in

colin_tlrc_1x1x1.nii.gz -out higresTal_T12standard -omat

higresTal_T12standard.mat

 

However, my attempts to apply the transform matrix to the Talairach

mask have resulted in inaccurate results; the coordinate results

differ too widely from known coordinates from Talairach coordinates

either converted to MNI coordinates with tal2icbm_fsl or to Talairach

label coordinates in fslview  MNI space.

 

I have tried to follow directions outlined on the FLIRT FAQ

http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT/FAQ#How_do_I_transform_a_mask_with_FLIRT_from_one_space_to_another.3F

but must be making some errors.

 

Any recommendations on how to apply the transform to the Talairach

space mask would be much appreciated.

 

Best,

Charles

 

On Tue, Aug 9, 2016 at 2:09 PM, Charles Leger <[log in to unmask]> wrote:

Thank you Colin. This is very helpful...

 

Best,

Charles

 

On Tue, Aug 9, 2016 at 1:04 PM, Charles <[log in to unmask]> wrote:

FSL experts,

 

Recently I posted a question asking how to transform a mask created in Talairach space to MNI space - all data in a current project will ultimately be in MNI space for  initial analysis in FSL. Taliairach coordinates can be converted to MNI space and subsequently a sphere mask can be made in FSL but it would be preferable to convert to MNI space an actual Talairach space mask made for the structure in question (a thalamic nucleus); the thalamic nucleus in question is not currently available in MNI space.

 

While the FLIRT (FNIRT) FAQ instructions (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT/FAQ#How_do_I_transform_a_mask_with_FLIRT_from_one_space_to_another.3F ) work flawlessly for transforming masks between spaces, converting a mask from a different standard  (Talairach) appears to involve more steps (FNIRT).

 

Again, any suggestions would be much appreciated.

 

Best,

Charles