A colleague of mine already preprocessed our DTI-data using qisprep. Now the only thing that I want to do is to run the reconstruction + fibertracking workflow (so that I don’t need to run the time consuming preprocessing). For this I am using the --recon_input
argument to tell qsiprep where it can find the preprocessed dataset. According to the docs this “option skips qsiprep”. However, I was surprised to find another qsiprep folder in my output directory next to my qsirecon folder. Is this normal behavior? Intuitively I would expect that the qsirecon-worklow simply grabs all the data that it needs but does not save another qsiprep folder. Here’s my script:
#############################################################
## Run qsiprep reconstruction for one subject
#############################################################
# analysis-settings
data_dir_server="/path/to/bids_dataset"
work_dir_server="/path/to/my/cache"
custom_atlases="/path/to/my/custom/atlas"
output_dir_server="/path/to/my/output"
recon_spec_dir="/path/to/my/custom/pipeline"
nthreads=64
omp_nthreads=16
mem_mb=30000
# run qsirecon
singularity run --cleanenv \
-B $custom_atlases:/atlas/qsirecon_atlases \
-B $data_dir_server \
-B $output_dir_server \
-B $recon_spec_dir \
/csp-tools/singularity_images/qsiprep_0.14.3.sif \
$data_dir_server/rawdata $output_dir_server participant \
--recon_input $data_dir_server/derivatives/qsiprep \
--recon_spec $recon_spec_dir/dsi_studio_gqi_with_GlasserTianS1.json \
--output-resolution 1 \
--skip-bids-validation \
--fs-license-file $data_dir_server/derivatives/license.txt \
--work-dir $work_dir_server \
--nthreads $nthreads \
--omp_nthreads $omp_nthreads \
--mem_mb $mem_mb \
--participant_label INDI1W934