Dear Edward, Try deleting: /home/chang/GBM_Data/T1_template/Template_MNI_Normal122_sc_age19-40_tirq_1.0mm_T1_scalp_trip_synthseg.nii and /home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synthseg/042/pre_042_0000_synthseg.nii.gz And then run the same command. Easy_reg will create the right segmentations for you. Cheers, /Eugenio
-- Juan Eugenio Iglesias http://www.jeiglesias.com From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of r04458...@ntu.edu.tw <r04458...@ntu.edu.tw> Date: Sunday, March 31, 2024 at 3:55 AM To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg with --parc option ? External Email - Use Caution Hello Freesurfer Developpers, I attempted to run mri_easyreg (Freesurfer 7.4) between two images. After I ran mri-easyreg adding these images (--ref_seg --flo_reg), I get again the > no cortical parcels. The following is the command I used and the error code. What did I do wong? Any hints? Thanks in advance for your help. Best, Edward mri_easyreg --ref /home/chang/GBM_Data/T1_template/Template_MNI_Normal122_sc_age19-40_tirq_1.0mm_T1_scalp_trip.nii --flo /home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only/pre_042_0000.nii.gz --ref_seg /home/chang/GBM_Data/T1_template/Template_MNI_Normal122_sc_age19-40_tirq_1.0mm_T1_scalp_trip_synthseg.nii --flo_seg /home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synthseg/042/pre_042_0000_synthseg.nii.gz --ref_reg /home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synthseg/042/pre_042_ref_reg.nii.gz --flo_reg /home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synthseg/042/pre_042_flo_reg.nii.gz --fwd_field /home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synthseg/042/pre_042_FWF.nii.gz --bak_field /home/chang/GBM_Data/GBM_original/20231223_1/Pre/Kuo/Brain_only_synthseg/042/pre_042_BWF.nii.gz 2024-03-31 15:50:23.731218: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used. 2024-03-31 15:50:23.752531: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used. 2024-03-31 15:50:23.752807: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations. To enable the following instructions: AVX2 AVX_VNNI FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags. 2024-03-31 15:50:24.041622: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT using 1 thread Segmentation of reference image already exists; reading from disk Error: No cortical labels found; does the segmentation include cortical parcels?
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