Summary of what happened:
Hi, experts. I want to run reconstruction on the minimally preprocessed HCP-YA DWI data and I’m a bit confused about how to feed the HCP-YA preprocessed DWI data into the QSIrecon pipeline. The preprocessed DWI data for each subject:
.
├── Diffusion
│ ├── bvals
│ ├── bvecs
│ ├── data.nii.gz
│ ├── eddylogs
│ │ ├── eddy_unwarped_images.eddy_movement_rms
│ │ ├── eddy_unwarped_images.eddy_outlier_map
│ │ ├── eddy_unwarped_images.eddy_outlier_n_sqr_stdev_map
│ │ ├── eddy_unwarped_images.eddy_outlier_n_stdev_map
│ │ ├── eddy_unwarped_images.eddy_outlier_report
│ │ ├── eddy_unwarped_images.eddy_parameters
│ │ ├── eddy_unwarped_images.eddy_post_eddy_shell_alignment_parameters
│ │ └── eddy_unwarped_images.eddy_restricted_movement_rms
│ ├── grad_dev.nii.gz
│ └── nodif_brain_mask.nii.gz
└── T1w_acpc_dc_restore_1.25.nii.gz
I have organized the DWI files (data, bvec, and bval) and T1w into the BIDS format:
.
├── dataset_description.json
└── sub-001
├── anat
│ └── sub-001_T1w.nii.gz
└── dwi
├── sub-001_dwi.bval
├── sub-001_dwi.bvec
└── sub-001_dwi.nii.gz
I encountered an error with the BIDS format. Should I use the BVAL and BVEC files from the unprocessed DWI folder?
Command used (and if a helper script was used, a link to the helper script or the command generated):
export HOME=/home/data/user7/HCPYA_Diffusion_Preprocessed/test
docker run -ti --rm \
--gpus all -e NVIDIA_DRIVER_CAPABILITIES=compute,utility -e NVIDIA_VISIBLE_DEVICES=all \
-v $HOME/hcpya_dwi:/data \
-v $HOME/output:/output \
-v $HOME/freesurfer:/freesurfer_output \
-v $HOME/working_dir:/working_dir \
pennbbl/qsiprep:0.20.0 \
/data /output participant \
--output-resolution 1.5 \
--recon_input /data
--recon-input-pipeline hcpya \
--freesurfer-input /freesurfer_output \
--recon-spec mrtrix_multishell_msmt_ACT-hsvs \
--recon-only \
--fs-license-file /usr/local/freesurfer/license.txt \
-w /working_dir -v -v
Version:
pennbbl/qsiprep:0.20.0
Environment (Docker, Singularity / Apptainer, custom installation):
Docker
Data formatted according to a validatable standard? Please provide the output of the validator:
1: [ERR] Each row in a .bvec file should contain the same number of values. (code: 46 - BVEC_ROW_LENGTH)
2: [ERR] .bval and .bvec files must be single space delimited and contain only numerical values. (code: 47 - B_FILE)
Screenshots / relevant information:
sub-001_dwi.bval.txt (1.3 KB)
sub-001_dwi.bvec.txt (9.3 KB)