dMRI lesion-load structural connectome

Generates a whole-brain structural connectome, characterizing the white matter connections between grey matter areas. Combining the capabilities of T1-based morphology and dMRI-based tractography, the structural connectome tool enables the quantification of brain connectivity between different the cortical and sub-cortical regions of interest (ROIs).

T1-based ROI Parcellation
dMRI-based Tractography

Connectivity matrix circular plot

The full workflow includes:

  • DICOM files to NIfTI conversion and reorientation to standard template images (MNI152). It will extract the required files (if possible) to do the dmri preprocessing step (eddy) and the gradient tables. If nifti files or gradient tables are found in the input, it will reorient to standard and output the files.
  • Automatic lesion segmentation from T2-FLAIR hyperintensities (see Lesion Segmentation Tool - LPA)
  • Semi-automatic lesion mask QC and editing (see Manual & semi-automatic lesion-mask editing)
  • Automatic lesion-filling of lesions in the T1 image with values of surrounding healthy tissue (see Lesion Filling)
  • Rigid alignment of the T2-FLAIR acquisition to the T1-weighted volume.
  • dMRI preprocessing includes denoising, gibbs ringing correction, eddy correction, motion correction, bias field correction, distortion correction (if gradient field maps are available) and ACPC alignment.
  • Brain mask extraction in dMRI space and tensor computation, plus derivation of different scalar measures: FA, AD, MD (ADC), RD, Cl, Cs, Cp.
  • ANTs cortical volumetry over the structural T1w image to extract the tissue segmentation file.
  • Applies an atlas to the segmented mask of the cortex (gray matter + subcortical gray matter + brainstem + cerebellum).
  • Align the diffusion image to the T1.
  • Estimate the diffusion model. Constrained spherical deconvolution model, multi-tissue and multi-shell processing is available. Does nothing if the data is DTI.
  • Perform probabilistic or deterministic tractography over the diffusion model. ACT (Anatomically constrained tractography; using the 5tt format from mrtrix) is available.
  • Estimates the connectome using the tractography and the registered labels. Outputs the normalized connectomes by volume and/or fibber length and in matrix and vector format. Connectome analysis via different graph-based measures: characteristic path length, density, node degree, assortativity, modularity, efficiency, and clustering coefficient (local and global).
  • Compute four lesion load measures over the connections between nodes:
  • Volumetric Binary damage: Counts how many lesion voxels overlap with the fibber bundle over the total number of voxels of the fibber bundle
  • Volumetric Weighted damage: Adds the fibber map image voxels (how many fibbers cross in each voxel) that overlay with the lesions over the sum of all the fibber map voxels.
  • Number of damaged fibbers: Number of fibbers crossing lesion voxels over the total number of fibbers.
  • Length-weighted damaged fibbers: Length of the damaged fibbers added up divided by the sum of the lengths of all the fibbers in the bundle
  • PDF final report including the connectome matrix, glass brain visualization, graph-based measures tables, morphology tables.

Required inputs:

  • T1: anatomical 3D image
  • Isotropic resolution recommended
  • Must be labeled as 'T1' modality
  • T2-FLAIR: anatomical 3D image
  • Isotropic resolution recommended
  • Must be labeled as 'T2' modality
  • dMRI: diffusion 4D image (DTI or HARDI).
  • Isotropic resolution recommended.
  • Must be labeled as 'DTI' or 'HARDI' modality.
  • Gradients: gradient table (optional if dMRI is DICOM).
  • MRtrix format supported: file must be labeled as 'gradient_table'.
  • BVEC/BVAL FSL format supported: files must be labeled as 'bvec' and 'bval'.

Minimum input requirements:

  • Image must contain full brain DWI dataset.
  • For optimal result reliability, an isotropic resolution is highly recommended
  • T1 and T2 recommended resolution: 1 mm isotropic.
    • T1 and T2 minimum reliable resolution: 2mm isotropic.
  • dMRI recommended resolution: 2 mm isotropic.
    • dMRI minimum reliable resolution: 3 mm isotropic.
  • If DTI image must have at least 7 volumes (1 b0 and 6 diffusion volumes).
  • If HARDI image must have at least 21 volumes (1 b0 and 20 diffusion volumes).
  • For optimal preprocessing reliability, 1 b0 image is recommended every 10 gradient volumes.

Optional inputs:

  • GFMs: Gradient field-maps, recommended (magnitude image and phase image).
  • Same resolution and FOV as dMRI image recommended.
  • Files must be labeled 'gfm_magnitude' and 'gfm_phase' respectively.



  • Check when data is skull stripped (checkbox): Enable this if the input data is skull stripped (default unchecked)
  • Change image resolution (checkbox): Changes the voxel size to isotropic resolution, defined in the next setting (default checked)
  • Isotropic voxel final size (mm) (integer): Define new isotropic resolution for the T1 image (default: 1)
  • ACPC alignment and remove subject face (checkbox): enable defacing step
  • Output transformation mat (checkbox): get the transformation matrix in the output container.


  • Preferred DICOM to NIfTI conversion tool (drop-down selection): The selected tool will be tried first to convert DICOM to NIfTI. If the conversion fails, the other options will be tried sequentially until a successful conversion.
    • DCM2niix (Default)
    • Mrtrix
    • DCM2nii
    • diffunpack
    • MRIConvert (mcverter)
  • Reorient images to standard space (checkbox)


  • Lesion filling tool (single choice): Options are:
  • ANTs (by default)
  • FSL
  • In-house python algorithm


  • Compute thickness map (checkbox): Perform additional cortical thickness on T1 (default unchecked)


  • Use transformation matrix if available (must be disabled)
  • Keep original dimensions (must be disabled)
  • Apply mask if available (must be disabled)
  • Keep image in input space (must be disabled)


  • Binarize probability maps (decimal value): Number between 0 and 1 to threshold the lesion maps. Default: 0.


  • Category Conf.
  • Lesion post-processing.


  • Identification prefix for the different lesions: Prefix that appears in the lesion cleanup editor.


  • FSL Tensor (checkbox): If the tensor input image comes from FSL the volumes must be reordered.


  • Do denoising (checkbox)(default checked)
  • Do Gibb ringing correction (checkbox)(default checked)

NOTE The following information about the sequence protocol is required for optimal pre-processing •Echo Spacing (s): The time between echoes in an echo planar image (EPI). •Echo Factor: also called Echo Train Length (ETL), the number of echoes acquired in a single repetition time (TR) •Acceleration factor: the number of EPI lines acquired in parallel •Echo Difference (s): (only needed if GFMs are provided), the difference in Echo Time (ET) between GFM acquisitions. Default value is typical for SIEMENS scanners

  • Do Eddy (checkbox)(default checked)
  • Do Fugue (checkbox)(default checked)
  • Use manual diffusion acquisition parameters (checkbox): Use the manually introduced diffusion acq. parameters (the next parameters)

Diffusion acquisition parameters: Usually obtained directly from the DICOMs' header

  • Echo Spacing (s) (float): The time between echoes in an echo planar image (EPI) (Default 0.0003ms)
  • Echo Factor (integer): Also called Echo Train Length (ETL), the number of echoes acquired in a single repetition time (TR) (default 100)
  • Acceleration Factor (integer): The number of EPI lines acquired in parallel (Default 1)
  • Echo Difference (s) (float) (only needed if GFMs are provided): The difference in Echo Time (ET) between GFM acquisitions. (default 0.00246 for SIEMENS acquisitions)
  • AC-PC alignment (checkbox)(default unchecked)
  • Resample dMRI image (checkbox)(default checked)
  • dMRI isotropic resampling resolution (mm) (float) Resamples the dMRI image to the indicated isotropic resolution in mm. (Default 2 mm)
  • Do bias field correction (checkbox)
  • Resample dMRI image (checkbox)
  • dMRI isotropic resampling resolution (mm) (default: 2)


  • Compute non-linear registration EPI to T1 (FA input required) to correct for distortion when gradient field maps are not available. We strongly recommend to visually inspect the results when this is selected. (checkbox) (default unchecked)


  • Brain atlas for parcellation (drop-down selection):
  • DKT40 (Mindboggle-101) (default)
  • AAL


  • Tracking algorithm type (drop-down selection)
  • Multi-tissue constrained spherical deconvolution (default)
  • Constrained Spherical Deconvolution (CSD)
  • Tensor


Track generation - Max. spherical harmonic order (drop-down selection): - 4 - 6 (default) - 8 - 10 - Tracking algorithm type (drop-down selection) - Deterministic - Probabilistic - Number of streamlines (integer) Number of streamlines to generate (default 1M) - Step size (mm) (0 for adaptative default) (float) (default 0)

Track stopping criteria - Use Anatomical constrained tractography (checkbox): Only works when Morphology results for ACT are passed as input (default checked) - Stopping angle (º) [0 for adaptive default] (integer) (default 0) - Min. streamline length (mm) [0 for adaptive default] (integer) (default 0) - Max. streamline length (mm) [0 for adaptive default] (integer) (default 0) - Min. FA/FOD cutoff (float) (default 0) More information about the adaptative results in: MRTRIX Docs

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