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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 CautionHi 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
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."
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