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.-o <output folder>, --output-dir=<output folder> <<BR>> Output directory - default = `<eddy_output_basename>.qc`. | |
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.-v, --verbose <<BR>> When set, display debug messages. | .`-o <output folder>, --output-dir=<output folder>` <<BR>> Output directory - default = `<eddy_output_basename>.qc`. .`-v, --verbose` <<BR>> When set, display debug messages. == Output == * `qc.json` <<BR>> Single subject database containing quality metrics and data info. * `qc.pdf` <<BR>> Single subject QC report. * `avg_b*.png` <<BR>> Image showing mid-sagittal, -coronal and -axial slices of each averaged b-shell volume. * `avg_b0_pe*.png` <<BR>> Image showing mid-sagittal, -coronal and -axial slices of each averaged pe-direction b0 volume. Generated when using the `-f` option. * `cnr*.png` <<BR>> Image showing mid-sagittal, -coronal and -axial slices of each b-shell CNR volume. Generated when CNR maps are available. * `vdm.png` <<BR>> Image showing mid-sagittal, -coronal and -axial slices of the voxel displacement map. Generated when using the `-f` option. * `eddy_msr.txt` <<BR>> Text file containing the volume-wise mask-averaged squared residuals. Generated when residual maps are available. * `vols_no_outliers.txt` <<BR>> Text file containing a list of clean volumes, based on the eddy squared residuals. To generate a version of the pre-processed dataset without outlier volumes, use: {{{ fslselectvols -i <eddy_corrected_data> -o eddy_corrected_data_clean --vols=vols_no_outliers.txt }}} = Running SQUAD = SQUAD expects a list of single-subject QC folders generated by QUAD. The study-wise tool has been designed to allow maximum flexibility in terms of QC capabilities. The most basic way to run `eddy_squad` after having pre-processed the dMRI dataset consists in running the following example command: {{{ eddy_squad <quad_folders> }}} This will result in the creation of a new folder, called `squad`. This will contain the study-wise QC report and database. |
WARNING This page is being edited in preparation for a new release
Contents
- Introduction
- Users Guide
The EDDY QC tools
The EDDY QC framework consists of two different tools that automatically perform QC both at the single subject and study-wise level.
QUAD (QUality Assessment for DMRI) generates single subject reports and stores the quality assessment indices for each subject.
SQUAD (Study-wise QUality Assessment for DMRI) reads all the single subject outputs from QUAD, generates study-wise reports and, optionally, enters these into a database. Moreover, SQUAD can optionally update single subject reports, indicating how the subject’s dataset compares to other data, using either a study-specific group database or a pre-generated database obtained from a different dataset. Lastly, SQUAD also allows to report QC indices based on user-provided variables.
The tools can be called from the command line using eddy_quad and eddy_squad.
Running QUAD
QUAD expects an EDDY output basename to identify the relevant output files that have been generated according to some user-specified options. If a feature, e.g., outliers detection and replacement, was not used, the outliers-related quality metrics will not be included in the final report nor added to the single-subject database. The most basic way to run eddy_quad after having pre-processed the dMRI dataset consists in running the following example command:
eddy_quad <eddy_output_basename> -idx <eddy_index_file> -par <eddy_acqparams_file> -m <nodif_mask> -b <bvals>
This will result in the creation of a new folder, called <eddy_output_basename>.qc. This will contain the single subject QC report and database, together with the slices included in the report stored as single image files.
List of input parameters
- Compulsory arguments:
<eddy_output_basename>
Basename for EDDY output-files, i.e., corrected images and QC files.-idx <eddy_index_file>, --eddyIdx=<eddy_index_file>
Text file containing indices linking each acquired volume to the acquisition parameters-par <eddy_acqparams_file>, --eddyParams=<eddy_acqparams_file>
Text file containing acquisition parameters-m <nodif_mask>, --mask=<nodif_mask>
Binary mask file for the whole brain or a specific region. All voxel-wise QC metrics consider entries only from the marked voxels.-b <bvals>, --bvals=<bvals>
b-values text file- Optional arguments:
-f <fieldmap>, --field=<fieldmap>
TOPUP estimated field (in Hz). When provided, QUAD will compute a voxel displacement map.-g <bvecs>, --bvecs=<bvecs>
b-vectors text file - use only when storing the EDDY residuals.-s <slspec>, --slspec=<slspec>
Text-file describing slice acquisition order.-o <output folder>, --output-dir=<output folder>
Output directory - default = <eddy_output_basename>.qc.-v, --verbose
When set, display debug messages.
Output
qc.json
Single subject database containing quality metrics and data info.qc.pdf
Single subject QC report.avg_b*.png
Image showing mid-sagittal, -coronal and -axial slices of each averaged b-shell volume.avg_b0_pe*.png
Image showing mid-sagittal, -coronal and -axial slices of each averaged pe-direction b0 volume. Generated when using the -f option.cnr*.png
Image showing mid-sagittal, -coronal and -axial slices of each b-shell CNR volume. Generated when CNR maps are available.vdm.png
Image showing mid-sagittal, -coronal and -axial slices of the voxel displacement map. Generated when using the -f option.eddy_msr.txt
Text file containing the volume-wise mask-averaged squared residuals. Generated when residual maps are available.vols_no_outliers.txt
Text file containing a list of clean volumes, based on the eddy squared residuals. To generate a version of the pre-processed dataset without outlier volumes, use:fslselectvols -i <eddy_corrected_data> -o eddy_corrected_data_clean --vols=vols_no_outliers.txt
Running SQUAD
SQUAD expects a list of single-subject QC folders generated by QUAD. The study-wise tool has been designed to allow maximum flexibility in terms of QC capabilities. The most basic way to run eddy_squad after having pre-processed the dMRI dataset consists in running the following example command:
eddy_squad <quad_folders>
This will result in the creation of a new folder, called squad. This will contain the study-wise QC report and database.