External Email - Use Caution 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<https://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 Costa<https://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 -0700<https://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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1gm8Mo90Xz5BNWI2qCZ6Q3l2guFyqznXM3Mc10zV67LMsh3dgp1qYggNc7OzO0cR3BDVCx2KvD4vsF8E8K_YxiyoEG_z_mQQdCT6SN7e-C7D5TWABM7svub-vsdKV1U5t8LGN8JTnVZuNJi1A7eX7hW2sQuxc4s5MFfv9gsC87XEIMk_yEEGwIFqrxoF6dTNIVtSCW-u7gkf2WU5bky-pVZhDNZCMiezi16ZIH6_dCpXB6cohD73JrNIKo9VL__JnvFq3uQ_4M6KfFzX1B7FItg/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 https://secure-web.cisco.com/12Agmx53cqZKs72ZRcgmLh2khJsG4EHKL-2xt0JtfedpJHMjFAp5qylyG-B7MR37XvPISkhGokg42umy9NkIAG11g31IlbB5PZ29fzeF7rsK3KDHS0NnQ-XQO5fTiQEoBzyQxMp4uYsZ-z4beMS4rzBr7QhLM272Q7NsmocAgZfUsoAO5Mdi3V4jzR_UArg2JSzU6dnWRlWxEzWFkeOt-iZeCm3_Gqj3WmPGtExZMGhM3gXSfl8ckm7nesrXZyyskzWph9ql4RgAk_FCFK1ahLQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <https://secure-web.cisco.com/12Agmx53cqZKs72ZRcgmLh2khJsG4EHKL-2xt0JtfedpJHMjFAp5qylyG-B7MR37XvPISkhGokg42umy9NkIAG11g31IlbB5PZ29fzeF7rsK3KDHS0NnQ-XQO5fTiQEoBzyQxMp4uYsZ-z4beMS4rzBr7QhLM272Q7NsmocAgZfUsoAO5Mdi3V4jzR_UArg2JSzU6dnWRlWxEzWFkeOt-iZeCm3_Gqj3WmPGtExZMGhM3gXSfl8ckm7nesrXZyyskzWph9ql4RgAk_FCFK1ahLQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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