Summary of what happened:
I want to use anat SSWarper images for qsiprep instead of the original T1w images. recon-all has been run. I have given a flag --anat-modality none as I had gotten a previous error which was asking for the T1w files. I get an error saying file ‘none’ not found. This means it requires some file and I was wondering how I can denote that.
Command used (and if a helper script was used, a link to the helper script or the command generated):
module load singularity
set -eu
umask 0002
# Configuration
subject=sub-002
version=0.22.1
# Directory structure
bids_root=/data/mgh-meditation/mihir/converted
bids_dir=${bids_root}/${subject}/bids
output_dir=/data/mgh-meditation/mihir/derivatives_qsi
work_dir=/data/mgh-meditation/mihir/work_qsiprep/${subject}
anat_dir=${bids_root}/${subject}/anat/SSWarper
# Create directories
cache_dir=${work_dir}/.cache
mkdir -p ${cache_dir}
mkdir -p ${output_dir}/{qsiprep,qsirecon}_${version}
mkdir -p ${work_dir}
# Paths
qsiprep_img=/data/mgh-meditation/mihir/qsiprep-${version}.sif
recon_spec=/data/mgh-meditation/mihir/recon_spec.json
fs_license=/data/mgh-meditation/mihir/freesurfer_output_final_anatSS/license.txt
cmd="singularity run --writable-tmpfs -e \
-B ${bids_dir},${output_dir},${work_dir},${cache_dir},${anat_dir},/data/mgh-meditation/mihir/freesurfer_output_final_anatSS/ \
${qsiprep_img} \
${bids_dir} \
${output_dir} \
participant \
--participant-label ${subject} \
-w ${work_dir} \
--fs-license-file ${fs_license} \
--anat-modality none \
--unringing-method mrdegibbs \
--ignore fieldmaps \
--output-resolution 1.25 \
--stop-on-first-crash \
--notrack \
--mem-mb 31500 \
--nthreads 16 \
--omp-nthreads 8 \
--recon-spec mrtrix_multishell_msmt_ACT-hsvs \
--skip-bids-validation \
--freesurfer-input /data/mgh-meditation/mihir/freesurfer_output_final_anatSS/"
recon_only=" --recon-only --recon-input ${output_dir}/qsiprep_${version}"
echo "Processing ${subject}"
if [ ! -e ${output_dir}/qsiprep_${version}/${subject}.html ]; then
eval ${cmd}
else
eval ${cmd}${recon_only}
fi
Version:
0.22.1
Environment (Docker, Singularity / Apptainer, custom installation):
Singularity
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):
file none does not exist .
--- Logging error ---
Traceback (most recent call last):
File "/opt/conda/envs/qsiprep/lib/python3.10/logging/__init__.py", line 1100, in emit
msg = self.format(record)
File "/opt/conda/envs/qsiprep/lib/python3.10/logging/__init__.py", line 943, in format
return fmt.format(record)
File "/opt/conda/envs/qsiprep/lib/python3.10/logging/__init__.py", line 678, in format
record.message = record.getMessage()
File "/opt/conda/envs/qsiprep/lib/python3.10/logging/__init__.py", line 368, in getMessage
msg = msg % self.args
TypeError: not all arguments converted during string formatting
Call stack:
File "<string>", line 1, in <module>
File "/opt/conda/envs/qsiprep/lib/python3.10/multiprocessing/forkserver.py", line 274, in main
code = _serve_one(child_r, fds,
File "/opt/conda/envs/qsiprep/lib/python3.10/multiprocessing/forkserver.py", line 313, in _serve_one
code = spawn._main(child_r, parent_sentinel)
File "/opt/conda/envs/qsiprep/lib/python3.10/multiprocessing/spawn.py", line 129, in _main
return self._bootstrap(parent_sentinel)
Screenshots / relevant information:
While checking the logs, the error occurs somewhere after the ‘eddy’.
Grateful for any help! Thanks!
Mihir