It looks like there are some extra characters before '-flo_seg' flag. The command line is split into 2 lines.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of r04458005@ntu.edu.tw Sent: Wednesday, December 27, 2023 4:02 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_easyreg error: No cortical labels found; does the segmentation include cortical parcels?

External Email - Use Caution Hello FreeSurfer Developers,

I'm attempting to run the mri_easyreg and I used the following command:

mri_easyreg --ref /home/chang/GBM_Data/T1_template/Template_MNI_Normal122_sc_age19-40_tirq_1.0mm_T1.nii --flo /home/chang/GBM_Data/GBM_original/20231223_1/Post/T1/Reg/r002_T1W.nii --ref_seg /home/chang/GBM_Data/T1_template/Template_MNI_Normal122_sc_age19-40_tirq_1.0mm_T1-1.nii --flo_seg /home/chang/GBM_Data/GBM_original/20231223_1/Post/T1/Reg/r002_T1W_synthseg.nii --flo_reg /home/chang/GBM_Data/GBM_original/20231223_1/Post/T1/Reg/r002_T1W.nii --fwd_field /home/chang/GBM_Data/GBM_original/20231223_1/Post/T1/Reg/FWF.nii.gz --bak_field /home/chang/GBM_Data/GBM_original/20231223_1/Post/T1/Reg/BWF.nii.gz --threads -1 --affine_only

ERROR: Error: Floating segmentation must be provided --flo_seg: command not found

I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use.

1) FreeSurfer version: freesurfer_ubuntu22-7.4.1 2) Platform: Ubuntu 22.04.3 LTS

Please help me. Thanks! -Edward