BRAIN_Mask

Brain Masking, mask file will be added to the global variables in the result file

Command:

dmriprep

Module version:

0.1

Module type:

prep

Attributes:

utility

Notes:

BRAIN_Mask README

Source:

dtiplayground/dmri/preprocessing/modules/BRAIN_Mask

Protocol options

method

Method to extract the brain

Type:

list

Default:

fsl

Choices:

• fsl – Use FSL for Brainmasking

• synthstrip – SynthStrip deep learning brain extraction (FreeSurfer’s mri_synthstrip if found, otherwise built in)

• hdbet – HD-BET deep learning brain extraction of the average b0 (hd-bet command, e.g. installed in a separate Python environment)

• medianOtsu – dipy median_otsu, median filter and Otsu threshold of the average b0

• customMask – Use custom Brainmasking

averagingMethod

Averaging method by which the source image is generated for the mask

Type:

list

Default:

idwi

Choices:

• direct_average – Direct average on baseline images. If no baseline is found then average whole volume

• idwi – Geometric mean of baseline images. If no baseline is found then whole images will be used.

betFractionalThreshold

FSL bet fractional intensity threshold (-f, between 0 and 1); smaller values give a larger brain outline, larger values a smaller one

Type:

float

Default:

0.5

Used when:

method is fsl

synthstripInput

Image SynthStrip is applied to

Type:

list

Default:

ad

Used when:

method is synthstrip

Choices:

• ad – Axial diffusivity of a DTI fit of the image (diffusion weighted volumes up to b=1500)

• b0 – Average of the baseline (b=0) images

synthstripBorder

Mask border threshold in mm (mri_synthstrip -b); larger values give a larger mask

Type:

float

Default:

1.0

Used when:

method is synthstrip

synthstripNoCSF

Exclude the CSF from the brain border (mri_synthstrip –no-csf)

Type:

boolean

Default:

false

Used when:

method is synthstrip

synthstripImplementation

FreeSurfer’s mri_synthstrip or the built-in version (torch; the model weights are downloaded on first use)

Type:

list

Default:

auto

Used when:

method is synthstrip

Choices:

• auto – FreeSurfer’s mri_synthstrip if found, otherwise the built-in version

• freesurfer – FreeSurfer’s mri_synthstrip (7.3+)

• builtin – SynthStrip network run in dtiplayground (torch)

synthstripPath

FreeSurfer home directory or path of mri_synthstrip; if empty, $FREESURFER_HOME and the PATH are searched

Type:

filepath-remote

Default:

not set

Used when:

method is synthstrip

hdbetDevice

Device HD-BET runs on

Type:

list

Default:

auto

Used when:

method is hdbet

Choices:

• auto – GPU (cuda) if the torch of hd-bet sees one, otherwise CPU

• cuda – GPU (cuda)

• cpu – CPU

hdbetTTA

Test time augmentation (mirroring); disabling it (–disable_tta) is faster, mainly on CPU, at a slight cost in quality

Type:

boolean

Default:

true

Used when:

method is hdbet

hdbetPath

Path of the hd-bet command or of the Python environment (or its bin directory) it is installed in; if empty, the environment of dtiplayground and the PATH are searched

Type:

filepath-remote

Default:

not set

Used when:

method is hdbet

medianOtsuRadius

Radius (in voxels) of the median filter applied before the Otsu threshold

Type:

integer

Default:

4

Used when:

method is medianOtsu

medianOtsuNumpass

Number of median filter passes

Type:

integer

Default:

4

Used when:

method is medianOtsu

medianOtsuDilate

Number of binary dilation iterations applied to the mask (0 for none)

Type:

integer

Default:

0

Used when:

method is medianOtsu

modality

Modality of the input image

Type:

list

Default:

t2

Choices:

• t2 – T2 Modality

• fa – Fractional Anistropy

customMaskPath

Provide custom mask to override default

Type:

filepath-remote

Default:

not set

Used when:

method is customMask