It looks like there are some extra characters before '-flo_seg' flag. The
command line is split into 2 lines.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of r04458...@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
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