External Email - Use Caution Dear Experts, I'm trying to understand what is the best input choice for running SAMSEG --recon in order to have the closest results as possible when compared against ASEG after executing (separately) an instance of recon-all all (and the raw input files in NIFTI format). I'm very well aware that ASEG and SAMSEG are different methods. I'm using the aseg.stats file as a results of the recon-all all command (here renamed as aseg.recon-all.stats for an easier identification). These stats should be my reference.
Currently I've run the samseg command using the following input variants: 1) raw input file (brain MP-RAGE sequence) converted into a mgz archive (Raw.mgz). samseg --t1w ./Raw.mgz --s 002_S_0685_DIRECT --recon --refmode t1w The corresponding results are attached into (samseg.direct.stats) 2) This time I've used the file T1.mgz which is one of the intermediate results generated after running recon-all -autorecon 1. Specifically, this is the output of (mri_normalize <https://secure-web.cisco.com/1JV3nYNrViePm1qpOtzuMUtCndnVtCut-gp7OyXxNuXIOkpE_qcI5f6sZ_QCwSghG1IFvH334gaAg87lJLYfCvB-5zg8wmDlsw6lAdt8aOlOIPUAjSprkajT7zne-FP-hzGKv9CYvWmcSS9XIenkvKBhlfbO8vOv-ei30mFEGRIZaagYtK1Cyf9wmm4QF6GEj7bEzNVr-YBpfnGSNYSLBmufOWzHUZ-r1QCtztrC9tGdBWY2qatrd7cfd8q57QFqlCEFUVwIesthj1klkWBKBIVP9AjfVSX4ZriNvoJLsVcZ6fSYSPrEW5jpjoBoeTUkDy39-cD7pRoNjCcQMll36FQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmri_normalize> -g 1 -mprage nu.mgz T1.mgz). samseg --t1w ./T1W/T1.mgz --s 002_S_0685_DIRECT_T1W --recon --refmode t1w The corresponding samseg.stats file is attached and called (samseg.direct.t1.stats). 3) this time I've used the file brainmask.mgz which is the last intermediate result generated after running recon-all -autorecon 1. Specifically, this is the output of mri_watershed <https://secure-web.cisco.com/1DjG5BDGTEbHYOWKmd4lc63SOmX8IrmziV9_NRWhpCskwO6lXP_OANTKjLP4P7zNcWyFmHcUAzXkrwvHQHxjel7Kt6VWmoFp0Dec-s6MAlL-nBlLBeauEFL4752dC7HNmXyvpFp8GB9mROITqzNZ0ZMNc5G-lQL2FfUV5IGX-p1DHRNN5Vw7G8qdIAeHIJYRhKRyuEqIzZ0afOXOYp79zF4m6WaEvzjf_-MVMKRTIk65x00-gMPz3jln6JODEdkkvNPc1Vad_tMdDHjoDPvBUPDKPPmc3p840hpjbk-e2W_eYsL1dczzFZsnkSX25piGNbpcwFN_z2Y_fei_T89237Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmri_watershed>. samseg --t1w ./brainmask.mgz --s 002_S_0685_DIRECT_BRAIN --recon --refmode t1w The corresponding samseg.stats file is attached and called (samseg.brain.stats). I've noticed that the SAMSEG stats file (samseg.brain.stats) as obtained when using the brainmask.mgz as input file is the closest with the ASEG statistics (aseg.recon-all.stats). I also observe that the unknown volume is the lowest (# Measure Unknown, 5329.102436, mm^3) when using brainmask.mgz as input for SAMSEG, whereas is higher (Measure Unknown, 325302.894793, mm^3) when using T1.mgz as input file and is the highest (Measure Unknown, 946924.354060, mm^3) for the raw input. I know that for running recon-all we use the raw input files (for example, in NIFTI format), but I wanted to know what is the best possible configuration for SAMSEG in terms of input file in order to have the closest match between SAMSEG and ASEG statistics. Could it be possible to use the intermediate result T1.mgz or brainmask.mgz as input file for running samseg command? Is it a technically correct procedure? Do we need to use only the raw data as input for running samseg --recon command? Hope this is clear Regards GS
aseg.recon-all.stats
Description: Binary data
samseg.direct.stats
Description: Binary data
samseg.direct.t1w.stats
Description: Binary data
samseg.brain.stats
Description: Binary data
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . 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.
