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Hi Gonzalo,


Assuming that you have run mri_robust_template and obtained longitudinally registered images (e.g., tp0_t1_reg.mgz, tp1_t1_reg.mgz, etc...), then you can co-register each additional contrast of each time point with the commands:

mri_coreg --mov tp0_flair.nii --ref tp0_t1_reg.mgz --reg tp0_FLAIRtoT1.lta
mri_vol2vol --mov tp0_flair.nii --reg tp0_FLAIRtoT1.lta --o tp0_flair_reg.mgz --targ tp0_t1_reg.mgz

for time-point 0 and

mri_coreg --mov tp1_flair.nii --ref tp1_t1_reg.mgz --reg tp1_FLAIRtoT1.lta
mri_vol2vol --mov tp1_flair.nii --reg tp1_FLAIRtoT1.lta --o tp1_flair_reg.mgz --targ tp1_t1_reg.mgz

for time-point 1, etcetera.

Stefano

[Freesurfer] Longitudinal SAMSEG with multi-contrast data

Gonzalo Rojas Costa Mon, 12 Jun 2023 10:21:51 -0700

        External Email - Use Caution        

Hi:
  How can I generate "tp1_flair_reg.mgz" image appeared in command
"run_samseg_long --timepoint tp0_t1_reg.mgz tp0_flair_reg.mgz --timepoint
tp1_t1_reg.mgz tp1_flair_reg.mgz --timepoint tp2_t1_reg.mgz
tp2_flair_reg.mgz --output outputDir/" ?

  Sincerely,


Gonzalo Rojas Costa

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