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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 datahttps://secure-web.cisco.com/1wqAljGN-HfqNgjoB_GLYISZdkqc0_9NrBWKfoyXxioxHK0i086v_G7kb-EdcMGoIPUAEHSdvPkQz-lY692l8eyZb8c8CdwbVSB5K3r4u_8hqWyqwv8JMla_SGWfbF1EDcRVocCeQ4pTBM4rAJwhV4NXX9AY7G6K0zckgUX69DrDuoQtFYL916VUplmbGg9RNVmDPf7GYjrJdGQhklMHCyiLVDYhenoJJD3Ubd7QE0thqIT7j-J0DNU-kfEIPa3MyTs29-t_RYarcPaeEK5zhqQ/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Dsubject%3A%2522%255C%255BFreesurfer%255C%255D%2BLongitudinal%2BSAMSEG%2Bwith%2Bmulti%255C-contrast%2Bdata%2522%26o%3Dnewest

Gonzalo Rojas Costahttps://secure-web.cisco.com/17xEk5nL7zi1KleESqeBlN3BTHFcZZZ5aIVXY_BJb6V_LkD5dTKpK4cASAUBx66ibh0Qt_bImFx7qr8Eny1_MsvDSJmsV46QSwA-b9tKQzXelXveXjWon4MZ-KABPgK7oXYZr4WXiyYvjnzCet-9t4ETZM1-G1wurINEFe4Vjq_lpE7cXTd_i3jBQa92auOuL5q6oC-Lm16sRymwIgqTfMLIvvz9sqnqPqq2E8OPyZhfPZigvs8cXyqhi0gR8j_aCms4OA2Ad608Xa11NGbrH0A/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Gonzalo%2BRojas%2BCosta%2522 Mon, 12 Jun 2023 10:21:51 -0700https://secure-web.cisco.com/1emebkgy5p75OaE8PVfVUI7Bh8WG2NzT6RocEeQ_clhqM6oqqBlNnDfLLSn_R_wFQGiTg6mr4tB060ZBicJUEo6VMizqZkfKEPV7MxOY-e9l44dKHbtc8855IACiBjo32uafOQP_FSazPFR6F5b681YMuSmGfItBU1Xh8jweIBZ0e12H6IIhrfRI38XsvkN88GPjBOKLqmtRhtE3xzti5JfG5ZU68OdDiGqAo84qSTowkhIeiSh6W2NgxWpWMZM2X4baTlVhn6dBw4w2o8HdQIQ/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Ddate%3A20230612

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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