Summary of what happened:
Hello,
I am reaching out regarding an issue that I am encountering while I attempt to create parcellations based on output files I have generated. Essentially, I have run a pipeline that:
(a) first conducts fMRIprep processing,
(b) which is then followed by XCPD processing, by using the --skip-parcellation option (as the default parcellation options does not include the “cabp718” parcellation scheme), and
(c) finally followed by a post-XCPD operation that computes three parcellations (schaefer456, gordon333, cabp718) and extracts FD information.
I used this pipeline to process >1000 HCD subjects. However, it looks like some processed subjects (~60) do not have the necessary *dtseries.nii files and which were identified while running the post-XCPD operation. I have pasted part of the function call that handles locating these various *dtseries.nii files. I was wondering if there is a way to fix this error.
Thanks,
Saptarshi
Command used (and if a helper script was used, a link to the helper script or the command generated):
mapfile -t subs < ${sub_list}
count=0
for sub in ${subs[@]} ; do
echo "### Processing ${sub} ###"
sub_id=$(echo ${sub} | awk -F"_" '{print $1}')
# check scan pattern
if [[ " ${run1_subs[*]} " == *" $sub "* ]] ; then
dtseries_name=ses-01_task-rest_run-01_space-fsLR_den-91k_desc-denoised_bold.dtseries.nii
outlier_file_name=ses-01_task-rest_dir-AP_run-01_outliers.tsv
mtion_file_name=ses-01_task-rest_dir-AP_run-01_motion.tsv
elif [[ " ${PA_subs[*]} " == *" $sub "* ]] ; then
dtseries_name=ses-01_task-rest_dir-PA_space-fsLR_den-91k_desc-denoised_bold.dtseries.nii
outlier_file_name=ses-01_task-rest_dir-PA_outliers.tsv
mtion_file_name=ses-01_task-rest_dir-PA_motion.tsv
else
# typical subs
dtseries_name=ses-01_task-rest_space-fsLR_den-91k_desc-denoised_bold.dtseries.nii
outlier_file_name=ses-01_task-rest_outliers.tsv
mtion_file_name=ses-01_task-rest_motion.tsv
fi
# check if xcpd completed
func_dir=${ceph_dir}/${sub}/xcpd/sub-${sub_id}/ses-01/func
func_file=${func_dir}/sub-${sub_id}_${dtseries_name}
outlier_file=${func_dir}/sub-${sub_id}_${outlier_file_name}
mtion_file=${func_dir}/sub-${sub_id}_${mtion_file_name}
if [ -f ${func_file} ]; then
# Specify output directory
out_dir=${ceph_dir}/${sub}/post_xcpd
if [ ! -d ${out_dir} ]; then
mkdir ${out_dir}
fi
# Call function to generate FC matrix
for p in ${parcels[@]}
do
gen_fc_matrix ${p} ${func_dir} ${sub_id} ${out_dir} ${func_file} ${outlier_file}
done
# Call function to extract FD column
extract_fd_column ${sub} ${mtion_file} ${out_dir}
count=$((count+1))
echo "!!! Processed: $count "
else
echo "... No func file!"
fi
done
Version:
xcp_d-0.10.6.sif
Environment (Docker, Singularity / Apptainer, custom installation):
Singularity / Apptainer
Data formatted according to a validatable standard? Please provide the output of the validator:
PASTE VALIDATOR OUTPUT HERE
Relevant log outputs (up to 20 lines):
PASTE LOG OUTPUT HERE