sct_dmri_moco¶
Motion correction of dMRI data. Some of the features to improve robustness were proposed in Xu et al. (https://dx.doi.org/10.1016/j.neuroimage.2012.11.014) and include:
group-wise (
-g
)slice-wise regularized along z using polynomial function (-param). For more info about the method, type:
isct_antsSliceRegularizedRegistration
masking (
-m
)iterative averaging of target volume
The outputs of the motion correction process are:
the motion-corrected dMRI volumes
the time average of the corrected dMRI volumes with b == 0
the time average of the corrected dMRI volumes with b != 0
a time-series with 1 voxel in the XY plane, for the X and Y motion direction (two separate files), as required for FSL analysis.
a TSV file with one row for each time point, with the slice-wise average of the motion correction magnitude for that time point, that can be used for Quality Control.
usage: sct_dmri_moco -i <file> -bvec <file> [-h] [-bval <file>]
[-bvalmin <float>] [-g <int>] [-m <file>] [-param <list>]
[-x {nn,linear,spline}] [-ofolder <folder>] [-r {0,1}]
[-v <int>] [-qc <folder>] [-qc-seg <file>]
[-qc-fps <float>] [-qc-dataset <str>] [-qc-subject <str>]
MANDATORY ARGUMENTS¶
- -i
Diffusion data. Example: dmri.nii.gz
- -bvec
Bvecs file. Example: bvecs.txt
OPTIONAL ARGUMENTS¶
- -bval
Bvals file. Example: bvals.txt
Default: “”
- -bvalmin
B-value threshold (in s/mm2) below which data is considered as b=0. Example: 50.0
Default: 100
- -g
Group nvols successive dMRI volumes for more robustness. Example: 2
Default: 3
- -m
Binary mask to limit voxels considered by the registration metric. You may also provide a softmask (nonbinary, [0, 1]), and it will be binarized at 0.5. Example: dmri_mask.nii.gz
Default: “”
- -param
Advanced parameters. Assign value with
=
, and separate arguments with,
.poly
[int]: Degree of polynomial function used for regularization along Z. For no regularization set to 0. Default=2.smooth
[mm]: Smoothing kernel. Default=1.metric
{MI, MeanSquares, CC}: Metric used for registration. Default=MI.gradStep
[float]: Searching step used by registration algorithm. The higher the more deformation allowed. Default=1.sample
[None or 0-1]: Sampling rate used for registration metric. Default=None.
- -x
Possible choices: nn, linear, spline
Final interpolation.
Default: “spline”
- -ofolder
Output folder. Example: dmri_moco_results
Default: “”
- -r
Possible choices: 0, 1
Remove temporary files. 0 = no, 1 = yes
Default: 1
- -v
Possible choices: 0, 1, 2
Verbosity. 0: Display only errors/warnings, 1: Errors/warnings + info messages, 2: Debug mode
Default: 1
- -qc
The path where the quality control generated content will be saved. (Note: Both
-qc
and-qc-seg
are required in order to generate a QC report.)- -qc-seg
Segmentation of spinal cord to improve cropping in qc report. (Note: Both
-qc
and-qc-seg
are required in order to generate a QC report.)- -qc-fps
This float number is the number of frames per second for the output gif images.
Default: 3
- -qc-dataset
If provided, this string will be mentioned in the QC report as the dataset the process was run on.
- -qc-subject
If provided, this string will be mentioned in the QC report as the subject the process was run on.