Summary of what happened:
Dear Neurostars community,
I would like to obtain output files that are the same as those described in the “Preprocessed data (QSIPrep derivatives)” section. Below are my raw data files, the code I used, and the tree structure of the output files I obtained. However, I found that my output files are missing the following files:
<source_entities>_space-ACPC_label-CSF_probseg.nii.gz
<source_entities>_space-ACPC_label-GM_probseg.nii.gz
<source_entities>_space-ACPC_label-WM_probseg.nii.gz
<source_entities>_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
<source_entities>_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz
<source_entities>_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz
<source_entities>_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz
<source_entities>_space-MNI152NLin2009cAsym_dseg.nii.gz
<source_entities>_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz
I thought these files would be automatically generated, but they did not appear. I would like to have a more complete set of output files. Can anyone help me identify where I might have gone wrong?
Command used (and if a helper script was used, a link to the helper script or the command generated):
The original data is organized as follows:
.
ses-20191107153150
|____ anat
|____ |____ sub-DOC0381_T1w.json
|____ |____ sub-DOC0381_T1w.nii.gz
|____ dwi
|____ |____ sub-DOC0381_dwi.bval
|____ |____ sub-DOC0381_dwi.bvec
|____ |____ sub-DOC0381_dwi.json
|____ |____ sub-DOC0381_dwi.nii.gz
|____ func
|____ |____ sub-DOC0381_task-rest_bold.json
|____ |____ sub-DOC0381_task-rest_bold.nii.gz
I would like to obtain output files that are the same as those described in the “Preprocessed data (QSIPrep derivatives)” section.
singularity run --cleanenv \
-B $wd:/wd \
-B $bids:/bids \
-B $output:/output \
-B $fs_license:/fs_license \
-B $templateflow:/templateflow \
/share/home/liuzebo/image/qsiprep_1.0.0.sif \
/bids /output participant -w /wd \
--participant-label sub-DOC${subj} \
--skip-bids-validation \
--nthreads 5 --mem-mb 20000 \
--anat-modality T1w \
--dwi-denoise-window auto \
--denoise-method dwidenoise \
--unringing-method mrdegibbs \
--b1-biascorrect-stage final \
--anatomical-template MNI152NLin2009cAsym \
--output-resolution 2 \
--intramodal-template-iters 0 \
--hmc-model eddy \
--fs-license-file /fs_license/license.txt \
--use-syn-sdc --force-syn \
--resource-monitor \
sub-<label>/[ses-<label>/]
anat/
# Brain mask derived from SynthStrip
<source_entities>_space-ACPC_desc-brain_mask.nii.gz
# Tissue-probability maps
<source_entities>_space-ACPC_label-CSF_probseg.nii.gz
<source_entities>_space-ACPC_label-GM_probseg.nii.gz
<source_entities>_space-ACPC_label-WM_probseg.nii.gz
# Tissue class map derived SynthSeg
<source_entities>_space-ACPC_dseg.nii.gz
# Bias field corrected T1w file, using ANTS' N4BiasFieldCorrection
<source_entities>_space-ACPC_desc-preproc_T1w.nii.gz
# The same files as above, but in the selected output space.
<source_entities>_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
<source_entities>_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz
<source_entities>_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz
<source_entities>_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz
<source_entities>_space-MNI152NLin2009cAsym_dseg.nii.gz
<source_entities>_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz
but I get
.
|____ log
|____ |____ 20250219-154558_609c8964-d843-46aa-bfaf-0fc74ba60eaa
|____ |____ |____ qsiprep.toml
|____ figures
|____ |____ sub-DOC0381_about.html
|____ |____ sub-DOC0381_summary.html
|____ ses-20191107153150
|____ |____ dwi
|____ |____ |____ sub-DOC0381_space-ACPC_desc-preproc_dwi.json
|____ |____ |____ sub-DOC0381_desc-confounds_timeseries.tsv
|____ |____ |____ sub-DOC0381_space-ACPC_desc-slice_qc.json
|____ |____ |____ sub-DOC0381_space-ACPC_model-eddy_stat-cnr_dwimap.nii.gz
|____ |____ |____ sub-DOC0381_space-ACPC_model-eddy_stat-cnr_dwimap.json
|____ |____ |____ sub-DOC0381_space-ACPC_desc-preproc_dwi.bval
|____ |____ |____ sub-DOC0381_space-ACPC_desc-preproc_dwi.bvec
|____ |____ |____ sub-DOC0381_space-ACPC_desc-preproc_dwi.b
|____ |____ |____ sub-DOC0381_space-ACPC_desc-preproc_dwi.b_table.txt
|____ |____ |____ sub-DOC0381_space-ACPC_desc-preproc_dwi.nii.gz
|____ |____ |____ sub-DOC0381_space-ACPC_dwiref.nii.gz
|____ |____ |____ sub-DOC0381_space-ACPC_desc-brain_mask.nii.gz
|____ |____ |____ sub-DOC0381_space-ACPC_desc-image_qc.tsv
|____ |____ anat
|____ |____ |____ sub-DOC0381_from-orig_to-anat_mode-image_xfm.txt
|____ |____ figures
|____ |____ |____ sub-DOC0381_conform.html
|____ |____ |____ sub-DOC0381_desc-summary_dwi.html
|____ |____ |____ sub-DOC0381_desc-denoising_dwi.svg
|____ |____ |____ sub-DOC0381_desc-unringing_dwi.svg
|____ |____ |____ sub-DOC0381_desc-seg_mask.svg
|____ |____ |____ sub-DOC0381_t1w2mni.svg
|____ |____ |____ sub-DOC0381_desc-carpetplot_dwi.svg
|____ |____ |____ sub-DOC0381_desc-coreg_dwi.svg
|____ |____ |____ sub-DOC0381_desc-sdc_b0.svg
|____ |____ |____ sub-DOC0381_desc-samplingscheme_dwi.gif
|____ |____ |____ sub-DOC0381_desc-biascorrpost_dwi.svg
|____ |____ |____ sub-DOC0381_desc-resampled_b0ref.svg
|____ anat
|____ |____ sub-DOC0381_from-anat_to-ACPC_mode-image_xfm.mat
|____ |____ sub-DOC0381_from-ACPC_to-anat_mode-image_xfm.mat
|____ |____ sub-DOC0381_space-ACPC_desc-preproc_T1w.nii.gz
|____ |____ sub-DOC0381_space-ACPC_desc-preproc_T1w.json
|____ |____ sub-DOC0381_space-ACPC_desc-brain_mask.nii.gz
|____ |____ sub-DOC0381_space-ACPC_desc-aseg_dseg.nii.gz
|____ |____ sub-DOC0381_space-ACPC_dseg.nii.gz
|____ |____ sub-DOC0381_from-ACPC_to-MNI152NLin2009cAsym_mode-image_xfm.h5
|____ |____ sub-DOC0381_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5
Version:
pennlinc/qsiprep:1.0.0
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):
PASTE LOG OUTPUT HERE