Hi Yujing,

I'll try to explain it more explicitly, I rerun my Code and show the results beyond attaching the Registration files too.

Consider a 3D-Nifti image called "Image.nii" the steps bellow executed in order:

0- Every time we Will generate a random Registration Matrix and Save it under the name "fsl.mat" which is the desired Registration matrix.

==============================================================================

fsl.mat :=

[[ 0.95509431, -0.28438761, 0.08317783, -5.        ]
 [ 0.2961434,   0.90701597, -0.29936787, -5.        ]
 [ 0.00969289,  0.31055712,  0.9505053,  -2.        ]
 [ 0.,          0.,          0.,          1.        ]]

==============================================================================

1- using a known registration matrice (called and attached in the first message and this message as "fsl.mat") resample the "Image.nii" to second Image called "fsl_resampled.nii"

Command : flirt -ref ./Image.nii -in ./Image.nii -applyxfm -init ./fsl.mat -out ./fsl_resampled.nii -interp spline

2- find out the registration matrices using Registration Methods, here we will use FSL, FreesSurefer, ANTs:

2.1. FSL Commands:

===============================================================================

Command : flirt -in ./Image.nii -out ./fslregistered.nii.gz -ref ./fsl_resampled.nii.gz -cost normmi -dof 6 -omat ./fslregistered.mat -interp spline

===============================================================================

fslregistered :

0.9551458402  -0.2842262621  0.08313877187  -5.029802253  
0.2959789517  0.9070999982  -0.2992758021  -5.014360215  
0.009646861275  0.3104593324  0.9505376886  -1.971170444  
0  0  0  1
=======================================================

The Registration Matrice in this Case Called "fslregistered.mat", using lta_convert we will make "fslregistered.lta"

Command : lta_convert --infsl ./fsl/fslregistered.mat --outlta ./fsl/fslregistered.lta --src ./Image.nii --trg ./fsl/fslregistered.nii.gz --ltavox2vox

===============================================================================

fslregistered.lta :

9.551459550857544e-01 -2.368552237749100e-01 6.928230822086334e-02 -4.191513061523438e+00 
3.551747798919678e-01 9.071001410484314e-01 -2.992758452892303e-01 -5.014381408691406e+00 
1.157622877508402e-02 3.104593753814697e-01 9.505378007888794e-01 -1.971183776855469e+00 
0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00

2.2. FreeSurfer Commands:

===============================================================================

Command : mri_robust_register --mov ./Image.nii --dst ./fsl_resampled.nii.gz --mapmov ./freesurfer.nii --lta freesurfer.lta --halfmov half-mov.nii --halfdst halfdst.nii --halfmovlta h1.lta --halfdstlta h2.lta --iscale --satit

===============================================================================
freesurfer.lta :
type      = 0 # LINEAR_VOX_TO_VOX
nxforms   = 1
mean      = 87.0000 129.0000 106.0000
sigma     = 10000.0000
1 4 4
9.550938606262207e-01 -2.369909435510635e-01 6.931482255458832e-02 -4.167178630828857e+00 
3.553738296031952e-01 9.070160388946533e-01 -2.993661761283875e-01 -4.999662876129150e+00 
1.163147203624249e-02 3.105554580688477e-01 9.505058526992798e-01 -2.000635147094727e+00 
0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00

================================================================================

The Registration Matrice in this Case Called "freesurfer.lta", using lta_convert we will do the conversion and build the FSL-Space "freesurfer.mat"

Command : lta_convert --inlta ./freesurfer/freesurfer.lta --outfsl ./freesurfer/freesurfer.mat --src ./Image.nii --trg ./fsl_resampled.nii.gz

========================================================
freesurfer.mat :
   0.95509410   -0.28438917    0.08317780   -5.00063801 
   0.29614490    0.90701610   -0.29936624   -4.99965954 
   0.00969290    0.31055552    0.95050597   -2.00067019 
   0.00000000    0.00000000    0.00000000    1.00000000

================================================================================

2.3. ANTs Commands:

================================================================================

Commands : antsRegistrationSyNQuick.sh -d 3 -f ./fsl_resampled.nii.gz -m ./Image.nii -o ants_ -t r

Using the ConvertTransform File we will make the "ants.txt"

Command : ConvertTransformFile 3 ./ANTS/ants_0GenericAffine.mat ./ANTS/ants.txt

================================================================================

ants.txt:

#Insight Transform File V1.0
#Transform 0
Transform: AffineTransform_double_3_3
Parameters: 0.9996357319973235 -0.01682948721742278 -0.021099091785527296 0.015864886388920783 0.9988573896699559 -0.045080156184165145 0.02183365965755943 0.04472900023162478 0.9987605357863502 -2.215029749904149 1.2122977228542815 -6.0667455324006445
FixedParameters: 5.195914900051355 -10.250280974097581 -6.670270481513606

================================================================================

Using lta_convert we first make "ants.lta"

Command: lta_convert --initk ./ANTS/ants.txt --outlta ./ANTS/ants.lta --src ./Image.nii --trg ./fsl_resampled.nii.gz --ltavox2vox

================================================================================

type      = 0 # LINEAR_VOX_TO_VOX
nxforms   = 1
mean      = 0.0000 0.0000 0.0000
sigma     = 1.0000
1 4 4
9.996357560157776e-01 -1.322073861956596e-02 1.819471642374992e-02 1.924201965332031e+00 
2.019538544118404e-02 9.988574385643005e-01 -4.472899809479713e-02 3.623344421386719e+00 
-2.531890943646431e-02 4.508015885949135e-02 9.987605214118958e-01 2.642463684082031e+00 
0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 
=================================================================================
Using the lta_convert we make the "ants.mat", the FSL-Spaced Registration matrix for ANTs
      Command: lta_convert --inlta ./ANTS/ants.lta --outfsl ./ANTS/ants.mat --src ./Image.nii --trg ./fsl_resampled.nii.gz
=================================================================================
  0.99963582   -0.01586489    0.02183366    2.30903101 
   0.01682949    0.99885744   -0.04472899    3.62335658 
  -0.02109909    0.04508016    0.99876052    2.64244890 
   0.00000000    0.00000000    0.00000000    1.00000000

As we could see there are problems in 'ants.lta' and 'ants.mat', I'm not sure Yet but I Suspect that the "PSR" Orientation of the Image Which is a Left-handed coordination System may cause that because in Another Experiment with "LAS" these problem had been occured but in another "RAS" Image the lta_convertor worked precisely with no problem.

The Registration Files are attached for More Information about Image's Geometry Sform's and Other ...

Best,

Yazdan

On Mon, 25 Sept 2023 at 17:16, Huang, Yujing <YHUANG43@mgh.harvard.edu> wrote:

External Email - Use Caution

Hi Yazdan,

I’m trying to understand the issues.

Can you specify the commands used to generate the matrices attached to your email? And give more details of the issues you are seeing?

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Yazdan Rezaee Jouryabi
Sent: Monday, September 25, 2023 1:49 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] lta_convert issue with ants Registration Matrix

External Email - Use Caution

Dear all, Hi

for checking registration i used fsl applyxfm on an Image(1)(Called Image.nii ) with specific Registration Matrice (Which we suppose to receive when we apply registration Methods) and Generate the "fsl_resampled.nii.gz" (Note: Image Orientations were LAS and in one other Experiment with also the same problem PSR)

for our case i will attach the "fsl.mat" (Desired Matrix)

using, fsl, freesurfer, and ants i got the correct results (let's call them "fslregistered.mat" and "freesurfer.mat" the converted lta to fsl-liked Matrix) Everything is OK till now

But the converted lta-like and fsl-like matrix for ANTs (Which are called ants.lta, and ants.mat) using the lines below:

- ConvertTransformFile 3 ./ANTS/ants_0GenericAffine.mat ./ANTS/ants.txt

- lta_convert --initk ./ANTS/ants.txt --outlta ./ANTS/ants.lta --src ./Image.nii --trg ./fsl_resampled.nii.gz --ltavox2vox

- lta_convert --inlta ./ANTS/ants.lta --outfsl ./ANTS/ants.mat --src ./Image.nii --trg ./fsl_resampled.nii.gz

As All Results Images (Registered Image of all Methods) are aligned perfectly i think that there might be some issues with lta_convert

Best Regards

Yazdan Rezaee J

P.S.
" I've checked the one similar mail on this topic and the conclusion on that was about (sform, qform) incompatibility but the affine matrices of S-form and q-form are equivalent in my case."

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