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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 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."