error runROBEX line 34
Hello! I have tried to run this program but it seems it fails at some point.
/opt/ROBEX/runROBEX.sh: line 34: 84 Killed ./ROBEX /Users/andraderenew/T1.nii.gz /Users/andraderenew/output_cerebellum/n4/T1_stripped.nii.gz /Users/andraderenew/output_cerebellum/n4/T1_mask.nii.gz Traceback (most recent call last): File "/usr/local/lib/python3.5/dist-packages/nibabel/loadsave.py", line 42, in load stat_result = os.stat(filename) FileNotFoundError: [Errno 2] No such file or directory: 'output_cerebellum/n4/T1_mask.nii.gz'
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/opt/n4/scripts/calc_weight_image.py", line 29, in obj = nib.load(args.mask) File "/usr/local/lib/python3.5/dist-packages/nibabel/loadsave.py", line 44, in load raise FileNotFoundError("No such file or no access: '%s'" % filename) FileNotFoundError: No such file or no access: 'output_cerebellum/n4/T1_mask.nii.gz' file output_cerebellum/n4/T1_mask_weight.nii.gz does not exist . /opt/n4/scripts/perform_n4.sh: line 84: 3524 Killed N4BiasFieldCorrection -d 3 -i T1.nii.gz -c [50x50x50x50,0.0005] -s 5 -o output_cerebellum/n4/T1_n4.nii.gz -w output_cerebellum/n4/T1_mask_weight.nii.gz -b [200] MNI registraion... ** ERROR (nifti_image_read): failed to find header file for 'output_cerebellum/n4/T1_n4.nii.gz' /opt/simple-pipeline/preprocessing_pipeline.sh: line 75: 3548 Segmentation fault (core dumped) reg_aladin -ref $mni_image -flo $n4_image -aff $affine -res $result -rmask $mni_brainmask -rigOnly -interp 3 -fmask $brain_mask > /dev/null ** ERROR (nifti_image_read): failed to find header file for 'output_cerebellum/n4/T1_n4.nii.gz' /opt/simple-pipeline/preprocessing_pipeline.sh: line 77: 3551 Segmentation fault (core dumped) reg_resample -trans $affine -ref $mni_image -flo $n4_image -res $result -inter 3 -pad 0 > /dev/null Cerebellum parcellation... 2022-12-05 18:10:03.591155: F tensorflow/core/platform/cpu_feature_guard.cc:36] The TensorFlow library was compiled to use AVX instructions, but these aren't available on your machine. /usr/local/bin/acapulco.sh: line 106: 3565 Aborted (core dumped) $(dirname $0)/predict.py -i $mni_image -o $parc_dir -l $LABELS -b $BBOX_MODEL -p $PARC_MODEL -s ${shape[@]} -c ${bbox_shape[@]} From output_cerebellum/mni/T1_n4_mni.nii.gz to output_cerebellum/parc/T1_n4_mni_seg.nii.gz Post processing... Traceback (most recent call last): File "/usr/local/lib/python3.5/dist-packages/nibabel/loadsave.py", line 42, in load stat_result = os.stat(filename) FileNotFoundError: [Errno 2] No such file or directory: 'output_cerebellum/parc/T1_n4_mni_seg.nii.gz'
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/usr/local/bin/cleanup_label_image.py", line 19, in obj = nib.load(args.image) File "/usr/local/lib/python3.5/dist-packages/nibabel/loadsave.py", line 44, in load raise FileNotFoundError("No such file or no access: '%s'" % filename) FileNotFoundError: No such file or no access: 'output_cerebellum/parc/T1_n4_mni_seg.nii.gz' From output_cerebellum/parc/T1_n4_mni_seg.nii.gz to output_cerebellum/parc/T1_n4_mni_seg_post.nii.gz Transform back to original space... [NiftyReg ERROR] Function: reg_tool_ReadAffineFile [NiftyReg ERROR] The affine file can not be read: output_cerebellum/mni/T1_n4_affine.txt [NiftyReg] Exit here. File: /tmp/niftyreg-git/reg-io/_reg_ReadWriteMatrix.cpp:145 ** ERROR (nifti_image_read): failed to find header file for 'output_cerebellum/parc/T1_n4_mni_seg_post.nii.gz' /usr/local/bin/acapulco.sh: line 121: 3631 Segmentation fault (core dumped) reg_resample -trans $inverse_aff -ref $image -flo $post -res $inverse -inter 0 -pad 0 > /dev/null From output_cerebellum/parc/T1_n4_mni_seg_post.nii.gz to output_cerebellum/T1_n4_mni_seg_post_inverse.nii.gz Calculate volumes of each region... Traceback (most recent call last): File "/usr/local/lib/python3.5/dist-packages/nibabel/loadsave.py", line 42, in load stat_result = os.stat(filename) FileNotFoundError: [Errno 2] No such file or directory: 'output_cerebellum/parc/T1_n4_mni_seg_post.nii.gz'
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/usr/local/bin/calc_volumes.py", line 21, in seg_obj = nib.load(args.input) File "/usr/local/lib/python3.5/dist-packages/nibabel/loadsave.py", line 44, in load raise FileNotFoundError("No such file or no access: '%s'" % filename) FileNotFoundError: No such file or no access: 'output_cerebellum/parc/T1_n4_mni_seg_post.nii.gz' From output_cerebellum/parc/T1_n4_mni_seg_post.nii.gz to output_cerebellum/T1_n4_mni_seg_post_volumes.csv