When trying to apply motion correction, the following error appears:
sct_dmri_moco -i denoised_patch2self.nii.gz -bvec bvecs -bval bvals -x spline
-- Spinal Cord Toolbox (5.3.0) sct_dmri_moco -i denoised_patch2self.nii.gz -bvec bvecs -bval bvals -x spline -- Input parameters: Input file ............ denoised_patch2self.nii.gz Group size ............ 3 Creating temporary folder (/tmp/sct-20210505170650.694281-moco-84mnd6p3) Copying input data to tmp folder and convert to nii... Get dimensions of data... 42 x 42 x 13 Data orientation: RAI Treated as axial Set suffix of transformation file name, which depends on the orientation: Orientation is axial, suffix is 'Warp.nii.gz'. The estimated transformation is a 3D warping field, which is composed of a stack of 2D Tx-Ty transformations Identify b=0 and DWI images... Traceback (most recent call last): File "/home/synapsi/sct_5.3.0/spinalcordtoolbox/scripts/sct_dmri_moco.py", line 225, in <module> main(sys.argv[1:]) File "/home/synapsi/sct_5.3.0/spinalcordtoolbox/scripts/sct_dmri_moco.py", line 210, in main fname_output_image = moco_wrapper(param) File "/home/synapsi/sct_5.3.0/spinalcordtoolbox/moco.py", line 217, in moco_wrapper param.verbose) File "/home/synapsi/sct_5.3.0/spinalcordtoolbox/scripts/sct_dmri_separate_b0_and_dwi.py", line 289, in identify_b0 bvals, bvecs = read_bvals_bvecs(fname_bvals, fname_bvecs) File "/home/synapsi/sct_5.3.0/python/envs/venv_sct/lib/python3.6/site-packages/dipy/io/gradients.py", line 46, in read_bvals_bvecs with open(this_fname, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: 'bvals'
However, bvals file exists and is placed in the working directory.