Hello, I’m new to bids & coding. I am working through part 1b of Stanfords BIDS Tutorial Series (BIDS Tutorial Series: Automate the Introductory Walkthrough | Stanford Center for Reproducible Neuroscience). I am currently spending a lot of time troubleshooting the code that is provided in the tutorial. For example, in order to complete Step 2, I had to change the code provided in the tutorial from:
####Anatomical Organization####
for subj in 2475376; do
echo “Processing subject $subj”###Create structure
mkdir -p {niidir}/sub-{subj}/ses-1/anat###Convert dcm to nii
#Only convert the Dicom folder anat
for direcs in anat; do
{dcm2niidir}/dcm2niix -o {niidir}/sub-{subj} -f {subj}%f%p {dcmdir}/{subj}/${direcs}
to
for subj in 2475376; do
echo “Processing subject $subj”;
done
for subj in 2475376; do
mkdir -p {niidir}/sub-{subj}/ses-1/anat**;**
done
for direcs in anat; do
[removed {dcm2niidir}]/**dcm2niix -o {niidir}/sub-{subj} -f {subj}%f%p {dcmdir}/{subj}/${direcs};**
done
Now I am on step 3, trying to rename the .nii and .json files, but I continue to receive the following error ouput:
ls: 2475376_anat_MPRAGE.json
2475376_anat_MPRAGE.nii: No such file or directory
mv: rename . to sub-2475376_ses-1_T1w.: Invalid argument
changed to sub-2475376_ses-1_T1w.
ls: 2475376_anat_MPRAGE.json
2475376_anat_MPRAGE.nii: No such file or directory
mv: rename . to sub-2475376_ses-1_T1w.: Invalid argument
changed to sub-2475376_ses-1_T1w.
I am confused because the code provided in the tutorial specifically mentions that the line Anat=$(ls MPRAGE) was included specifically to avoid the error “No such file or directory”.
Because I am beginner to bids and coding, I am struggling to troubleshoot the tutorial myself. My question is: is the code provided by the tutorial accurate? (i.e.: no syntax errors, commands appear in the correct), or is it merely a rough guideline?
For example, I am pretty confused why the third for-loop in step 2 included “${dcm2niidir}”? Is that a mistake, or am I misunderstanding something basic?
I would really appreciate any guidance in the topic.
Thank you so much in advance!