Difference between revisions of "DTI pre-processing"
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Diffusion Tensor Imaging depicts the anisotropy of tissue. | Diffusion Tensor Imaging depicts the anisotropy of tissue. | ||
| − | The acquisition protocol includes 6 or more diffusion weighted images (DWIs), one or more B null image (B0), a structural T1 image, and sometimes field maps (FM) that are used for susceptibility correction. | + | The acquisition protocol includes 6 or more diffusion weighted images (DWIs), one or more B null image (B0), a structural T1 image (eventually a brain mask), and sometimes field maps (FM) that are used for susceptibility correction. |
| − | The | + | The nipype script to generate the DTI is <code>perform_dti_processing.py</code> and its help message is the following: |
| + | <pre> | ||
| + | usage: perform_dti_processing.py [-h] -i dwis [dwis ...] -a bvals [bvals ...] | ||
| + | -e bvecs [bvecs ...] -t t1 [-m fieldmapmag] | ||
| + | [-p fieldmapphase] [-o output_dir] [-g] | ||
| + | [--rot rot] [--etd etd] [--ped [ped]] | ||
| + | [--rigid] | ||
| + | |||
| + | Perform Diffusion Model Fitting with pre-processing steps. Mandatory Inputs | ||
| + | are the Diffusion Weighted Images and the bval/bvec pair. as well as a T1 | ||
| + | image are extracted for reference space. The Field maps are provided so | ||
| + | susceptibility correction is applied. Values to use for the susceptibility | ||
| + | parameters: ## DRC ## (--ped=-y --etd=2.46 --rot=34.56) and ## 1946 ## | ||
| + | (--ped=-y --etd=2.46 --rot=25.92). Note that these values are indicative. | ||
| + | |||
| + | optional arguments: | ||
| + | -h, --help show this help message and exit | ||
| + | -i dwis [dwis ...], --dwis dwis [dwis ...] | ||
| + | Diffusion Weighted Images in a 4D nifti file | ||
| + | -a bvals [bvals ...], --bvals bvals [bvals ...] | ||
| + | bval file to be associated with the DWIs | ||
| + | -e bvecs [bvecs ...], --bvecs bvecs [bvecs ...] | ||
| + | bvec file to be associated with the DWIs | ||
| + | -t t1, --t1 t1 T1 file to be associated with the DWIs | ||
| + | -m fieldmapmag, --fieldmapmag fieldmapmag | ||
| + | Field Map Magnitude image file to be associated with | ||
| + | the DWIs | ||
| + | -p fieldmapphase, --fieldmapphase fieldmapphase | ||
| + | Field Map Phase image file to be associated with the | ||
| + | DWIs | ||
| + | -o output_dir, --output_dir output_dir | ||
| + | Output directory containing the registration result | ||
| + | Default is a directory called results | ||
| + | -g, --graph Print a graph describing the node connections | ||
| + | --rot rot Diffusion Read-Out time used for susceptibility | ||
| + | correction Default is 34.56 | ||
| + | --etd etd Echo Time difference used for susceptibility | ||
| + | correction Default is 2.46 | ||
| + | --ped [ped] Phase encoding direction used for susceptibility | ||
| + | correction (x, y or z) --ped=val form must be used for | ||
| + | -ve indicesDefault is the -y direction (-y) | ||
| + | --rigid Only use rigid registration for DWI (no eddy current | ||
| + | correction) | ||
| + | </pre> | ||
Revision as of 13:46, 25 August 2015
Diffusion Tensor Imaging depicts the anisotropy of tissue.
The acquisition protocol includes 6 or more diffusion weighted images (DWIs), one or more B null image (B0), a structural T1 image (eventually a brain mask), and sometimes field maps (FM) that are used for susceptibility correction.
The nipype script to generate the DTI is perform_dti_processing.py and its help message is the following:
usage: perform_dti_processing.py [-h] -i dwis [dwis ...] -a bvals [bvals ...]
-e bvecs [bvecs ...] -t t1 [-m fieldmapmag]
[-p fieldmapphase] [-o output_dir] [-g]
[--rot rot] [--etd etd] [--ped [ped]]
[--rigid]
Perform Diffusion Model Fitting with pre-processing steps. Mandatory Inputs
are the Diffusion Weighted Images and the bval/bvec pair. as well as a T1
image are extracted for reference space. The Field maps are provided so
susceptibility correction is applied. Values to use for the susceptibility
parameters: ## DRC ## (--ped=-y --etd=2.46 --rot=34.56) and ## 1946 ##
(--ped=-y --etd=2.46 --rot=25.92). Note that these values are indicative.
optional arguments:
-h, --help show this help message and exit
-i dwis [dwis ...], --dwis dwis [dwis ...]
Diffusion Weighted Images in a 4D nifti file
-a bvals [bvals ...], --bvals bvals [bvals ...]
bval file to be associated with the DWIs
-e bvecs [bvecs ...], --bvecs bvecs [bvecs ...]
bvec file to be associated with the DWIs
-t t1, --t1 t1 T1 file to be associated with the DWIs
-m fieldmapmag, --fieldmapmag fieldmapmag
Field Map Magnitude image file to be associated with
the DWIs
-p fieldmapphase, --fieldmapphase fieldmapphase
Field Map Phase image file to be associated with the
DWIs
-o output_dir, --output_dir output_dir
Output directory containing the registration result
Default is a directory called results
-g, --graph Print a graph describing the node connections
--rot rot Diffusion Read-Out time used for susceptibility
correction Default is 34.56
--etd etd Echo Time difference used for susceptibility
correction Default is 2.46
--ped [ped] Phase encoding direction used for susceptibility
correction (x, y or z) --ped=val form must be used for
-ve indicesDefault is the -y direction (-y)
--rigid Only use rigid registration for DWI (no eddy current
correction)
