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Hi Yazdan,
Thank you for the detailed explanation.
I’m wondering if you could send output of mri_info for Image.nii,
fsl_resampled.nii.gz, fslregistered.nii.gz, freesurfer.nii, and output from
ANTs.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Yazdan Rezaee Jouryabi
Sent: Friday, September 29, 2023 12:19 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] lta_convert issue with ants Registration Matrix
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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
<yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>> wrote:
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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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Yazdan Rezaee Jouryabi
Sent: Monday, September 25, 2023 1:49 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] lta_convert issue with ants Registration Matrix
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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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