Hello Julien
I am processing DTI of the spinal cord. I follow your guideline on the London course. I stuck at this step…
sct_dmri_moco -i dmri_crop.nii -bvecs.txt
-bvec file doesn’t exist: bvecs.txt
Could you please help.
Thank you
According to the help info for that function, you need to put -bvec before the name of the text file:
Hi,
the syntax was incorrect. It should be:
sct_dmri_moco -i dmri_crop.nii -bvec bvecs.txt
P.S. Order of param is not important
Hello Julien and Barryl
I put your command
sct_dmri_moco -i dmri_crop.nii -bvec bvecs.txt
Command-line usage error: Option -bvec file doesn’t exist: bvecs.txt
Aborted…
I didn’t work.
Any other suggetion?
it probably means that the file “bvecs.txt” does not exist. What is the output of ls?
Hi Julien,
What is Ls stand for?
I use these command:
sct_maths -i dmri.nii -mean t -o dmri_mean.nii
sct_propseg -i dmri_mean.nii -c dwi -qc ~/qc_singleSubj
sct_create_mask -i dmri_mean.nii -p centerline,dmri_mean_seg.nii -size 35mm
sct_crop_image -i dmri.nii -m mask_dmri_mean.nii -o dmri_crop.nii
Output were:
dmri_crop.nii
dmri_mean_centerline.nii
dmri_mean_seg.nii
dmri_mean.nii
dmri.nii
mask_dmri_mean.nii
ls lists the file present in your directory. I wanted to check if the file bvecs.txt was present or not. Based on your output, it looks like it is not present. So the problem is not the syntax, but it is that you have to provide a bvec file (and later, a bval file to compute the diffusion tensor).
If you used dcm2niix to convert your DICOM data, it automatically generates those files.