lta_convert issue with ants Registration Matrix

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Yazdan Rezaee Jouryabi

25 Sep 2023 25 Sep '23

1:48 a.m.

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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."

Attachments:

attachment.html (text/html — 2.0 KB)
ants.txt (text/plain — 408 bytes)
fslregistered.lta (application/octet-stream — 1.4 KB)
freesurfer.mat (application/octet-stream — 228 bytes)
ants.mat (application/octet-stream — 228 bytes)
fsl.mat (application/octet-stream — 179 bytes)
freesurfer.lta (application/octet-stream — 1.5 KB)
fslregistered.mat (application/octet-stream — 189 bytes)
ants.lta (application/octet-stream — 1.4 KB)

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Huang, Yujing

25 Sep 25 Sep

9:40 a.m.

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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-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 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

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."

Yazdan Rezaee Jouryabi

29 Sep 29 Sep

12:18 p.m.

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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 49.550938606262207e-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 49.996357560157776e-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."

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1CVysUaKA0QPJhHH2wwhYBipzUhFEaeL8kkwOtuATULgzm-... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1iXmC6GDGT_irmtwnhqZdBKSxywaeJC3Q1wdvh_a0KY5o7X... < https://secure-web.cisco.com/1iXmC6GDGT_irmtwnhqZdBKSxywaeJC3Q1wdvh_a0KY5o7X... .

Huang, Yujing

6 Oct 6 Oct

3:49 p.m.

External Email - Use Caution

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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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

External Email - Use Caution Hi Yujing, I'll try to explain it more explicitly, I rerun my Code and show the results beyond attaching the Registration files too.

[[ 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. ]] ==============================================================================

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

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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] lta_convert issue with ants Registration Matrix

External Email - Use Caution Dear all, Hi

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

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."

Yazdan Rezaee Jouryabi

8 Oct 8 Oct

10:03 a.m.

External Email - Use Caution

Hi Yujing,

Sure.

the results of applying mri_info are attached below

Bests, Yazdan.

On Fri, 6 Oct 2023 at 23:19, Huang, Yujing YHUANG43@mgh.harvard.edu wrote:

...

    External Email - Use Caution
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-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@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
   External Email - Use Caution        *
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."

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1BStSAxLh5BeN2L3rU2frK5cGS07arbjFgCFDCXjer8mI9E... https://secure-web.cisco.com/1CVysUaKA0QPJhHH2wwhYBipzUhFEaeL8kkwOtuATULgzm-ARVtRifTqrnuMch9mPrhoX5WsrgJCZI4n6LV0QrBOiwz8JOJSZcKXl0-srjhHE7Ez1eAdpgDrWIqslv1yZuu9lDDu4UrcCR_1k8-OHZM1lX5im7TD25ziCO5ibM6spWh-yZJ_pdgSrOWg3COhe2JLUiyCL3VPWaa-l3gJ-VY8E3fKgFi47mdINsuywYT2Z2bpFzMA0qVMOcxBZP6V2Jz-SpyfFbeS55S0r_f_lNm2JigMyuajjviAgHw-npf_6HYFs541IzQp4hzn0kOTN/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1Cw0A3cVjhHcWsRIekyy6Q8-imKvdraduISNe4Ov9uMpCll... https://secure-web.cisco.com/1iXmC6GDGT_irmtwnhqZdBKSxywaeJC3Q1wdvh_a0KY5o7X2IMOclXP4f0k-GqI_PRroMRHLYU-2PytqXKGTg6_fWW1KVDHATy0ENxJF3psR7lP7a-RRfcFNfBEjlwcIVKlvbWPxlCCMyKVbMe6U5Fh-MyOLPX0g_j4lWjXAjcWLJkRG0g4PBTK_xzSz904-Aq-5yTIzIoulIOOVdRa03bD2RdUbEfx4x44oD3QmrEeVyAQcHQXg97yGoNqncOG-pa601HCmc65kmd9kIqklmkjAhm1NA5O-PbF2zqMYfQYmUWbVziolYCOD5tYgNE9wx/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1Cw0A3cVjhHcWsRIekyy6Q8-imKvdraduISNe4Ov9uMpCll... https://secure-web.cisco.com/1iXmC6GDGT_irmtwnhqZdBKSxywaeJC3Q1wdvh_a0KY5o7X2IMOclXP4f0k-GqI_PRroMRHLYU-2PytqXKGTg6_fWW1KVDHATy0ENxJF3psR7lP7a-RRfcFNfBEjlwcIVKlvbWPxlCCMyKVbMe6U5Fh-MyOLPX0g_j4lWjXAjcWLJkRG0g4PBTK_xzSz904-Aq-5yTIzIoulIOOVdRa03bD2RdUbEfx4x44oD3QmrEeVyAQcHQXg97yGoNqncOG-pa601HCmc65kmd9kIqklmkjAhm1NA5O-PbF2zqMYfQYmUWbVziolYCOD5tYgNE9wx/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .

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Huang, Yujing

12 Oct 12 Oct

10:51 a.m.

External Email - Use Caution

Hi Yazdan,

Thanks for the information.

Is the “PSR/LAS/RAS Orientation of image” you mentioned the same ‘Orientation’ reported by mri_info? I believe the Orientation reported by mri_info tells the data ordering on disk. It is not the anatomical space. Both nii and mgz are RAS.

I tried the method described in this posting (https://secure-web.cisco.com/1APqgiyEgb8KoTku5P1376REqaOm8LWn2j_60Z3VrODJu7D...) registration_ras = flip_LPS_RAS @ registration_lps @ flip_LPS_RAS

registration_lps is ants.txt read in by lta_convert. I converted inv(registration_ras) to vox2vox using the vox2ras printed by mri_info. I got the same results as lta_convert.

I’m wondering if there are other ways to verify ants_0GenericAffine.mat and ants.txt generated by Ants.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Yazdan Rezaee Jouryabi Sent: Sunday, October 8, 2023 10:04 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] lta_convert issue with ants Registration Matrix

External Email - Use Caution Hi Yujing,

Sure.

the results of applying mri_info are attached below

Bests, Yazdan.

On Fri, 6 Oct 2023 at 23:19, Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote:

External Email - Use Caution 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] lta_convert issue with ants Registration Matrix

External Email - Use Caution Hi Yujing, I'll try to explain it more explicitly, I rerun my Code and show the results beyond attaching the Registration files too.

[[ 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. ]] ==============================================================================

0.9551458402 -0.2842262621 0.08313877187 -5.029802253

0.2959789517 0.9070999982 -0.2992758021 -5.014360215

0.009646861275 0.3104593324 0.9505376886 -1.971170444

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

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

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

#Insight Transform File V1.0

#Transform 0

Transform: AffineTransform_double_3_3

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

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.edumailto: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

External Email - Use Caution Dear all, Hi

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

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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Yazdan Rezaee Jouryabi

18 Oct 18 Oct

11:20 a.m.

External Email - Use Caution

Hi Yujing, 90 I mean that i had use "lta_convert" in two setup, 1) Images in RAS Orientation (Worked Well) 2) Images in "LAS/PSR" Orientation (Issues Happened here)

and Yes By definition nii, is defined in RAS+ so if we take a look at T_Vox2anatomical (S_rows (Sform), or quaternions (qform)) Which are stored in the header we could interpret it as mri_info does too, and says that all are in LAS orientation.

I thought that as "LAS-PSR" both are left-handed coordinate systems the program might have some issues with this Type of orientation and work Ok with right handed Images.

The Second guess might be usage of S-forms by one program and qform by the Other one. as it is stated here https://secure-web.cisco.com/1-25w9APT0HgxT9N-EfI7mMc3icOz7cv81LXfb_b6INmne_...

Best, Yazdan

On Thu, 12 Oct 2023 at 18:22, Huang, Yujing YHUANG43@mgh.harvard.edu wrote:

...

    External Email - Use Caution
Hi Yazdan,

Thanks for the information.

Is the “PSR/LAS/RAS Orientation of image” you mentioned the same ‘Orientation’ reported by mri_info? I believe the Orientation reported by mri_info tells the data ordering on disk. It is not the anatomical space. Both nii and mgz are RAS.

I tried the method described in this posting (*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1Ge3sBzHTtpKPPBh9OiSTIgwYz1_Beh4d9YQJtgo5XKYxA2... https://secure-web.cisco.com/1APqgiyEgb8KoTku5P1376REqaOm8LWn2j_60Z3VrODJu7DE6KX_dDgXHnyeNktNrvoY9UE8pztcC7TCnb9h1PgIAXAP6kEd4Gd_C0ixAxfgnBJlou_FkCewSW8_ccaXgIndWa-TX4_0jh53UNXJJWnohUqlbf2uexaNApI9yRCI9Gc05xXT4w5kh-xBOJ6yQ0TBjjMzxGKeQojzPYME53MhQwIt2Rq_rcHXbAkV3NMfjxZvvtrICQCv6QrXBdAX9xMR0IqW0uqjjVP1vDsXuQQ/https%3A%2F%2Fstackoverflow.com%2Fquestions%2F71441883%2Fhow-to-get-transformation-affine-from-itk-registration)

registration_ras = flip_LPS_RAS @ registration_lps @ flip_LPS_RAS

registration_lps is ants.txt read in by lta_convert. I converted inv(registration_ras) to vox2vox using the vox2ras printed by mri_info. I got the same results as lta_convert.

I’m wondering if there are other ways to verify ants_0GenericAffine.mat and ants.txt generated by Ants.

Best,

Yujing

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Yazdan Rezaee Jouryabi *Sent:* Sunday, October 8, 2023 10:04 AM *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,

Sure.

the results of applying mri_info are attached below

Bests,

Yazdan.

On Fri, 6 Oct 2023 at 23:19, Huang, Yujing YHUANG43@mgh.harvard.edu wrote:
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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-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@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 YHUANG43@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-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
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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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Huang, Yujing
Yazdan Rezaee Jouryabi