Important Links and things to know for the brainlife.io sections

Tutorial project: https://brainlife.io/project/5ae916e7f446980028b15eb3

• Contains the following from 3 Cam-CAN subjects

  • anat/t1w
  • anat/t2w
  • dwi
  • func/task (rest)
  • meeg (rest)

Tutorial project (with derivatives already generated): https://brainlife.io/project/64a314743a63cf17374ec653/pipeline

• Contains the following from 3 Cam-CAN subjects
  • anat/t1w
  • anat/t2w
  • neuro/dwi
  • func/task
  • neuro/meeg
  • transform/nifti
  • parcellation/volume
  • parcellation/surface-deprecated
  • neuro/mask
  • html
  • neuro/regressors
  • neuro/csd
  • neuro/tensor
  • neuro/track/tck
  • neuro/wmc
  • neuro/tractmeasures
  • neuro/streamline-weights
  • neuro/conmat
  • neuro/labels
  • raw
  • neuro/network
  • neuro/net-stats
  • neuro/parc-stats
  • neuro/timeseries

Structural preprocessing steps and apps:

1. FSL Anat (T1w)
   1. Reorient = true
   2. Crop = true
   3. Bias = true
2. FSL Anat (T2w)
   1. Reorient = true
   2. Crop = true
   3. Bias = true
3. Freesurfer 7.3.2
   1. Hippocampal = true
   2. Thalamicnuclei = true
   3. localGI = true
4. Multi-atlas Transfer Tool (w/ surface output)
   1. Atlas = hcp-mmp-b (glasser)
5. Multi-atlas Transfer Tool (w/ surface output)
   1. Atlas = yeo17dil (yeo)
6. Tissue type segmentation (generates white matter gray matter boundary for tracking)

Diffusion preprocessing steps and apps:

1. QSIPrep
   1. Output_resolution = 1.0
   2. Syn_scd = true
   3. Testing whether x flip is needed for this data or not
2. FSL Brain Extraction (BET) on DWI
   1. fthreshold = 0.3
3. Fit Constrained Deconvolution Model for Tracking
   1. Ensemble = true
4. Fit Tensor Model using MRTrix3
5. Anatomically Constrained Tractography using precomputed 5tt & CSD
   1. Min_length = 25
   2. Max_length = 250
   3. Num_fibers = 50,000 (XX total)
   4. Ensemble = true
   5. imaxs = 8
   6. Curves = 5, 10, 20, 40 80
   7. Do_dtdt = true
   8. Do_detr = true
   9. Do_prb2 = true
6. White matter anatomy segmentation
7. Remove Tract Outliers
   1. centroidSD = 4
   2. lengthSD = 4
   3. maxIter = 5
8. Tract Analysis Profiles
   1. Numnodes = 200
9. Tractography Quality check
10. Compile tract macro-structural and profile data
11. Compute streamline weights using SIFT2
12. Structural Connectome MRTrix3 (SCMRT)
13. Conmat to network
14. Network Measurements
15. Extract network statistics and connectivity matrices from network datatype
16. Cortex Tissue Mapping (Native & Template Space)
17. Compute summary statistics of diffusion measures mapped to cortical surface - Freesurfer computations
    1. Input hcp-mmp-b parcellation
18. Compute summary statistics of diffusion measures mapped to cortical surface - Freesurfer computations
    1. Input yeo17dil parcellation

Functional preprocessing steps and apps:

1. fMRIPrep - Volume Output
2. fMRI Timeseries Extraction
3. Time series to network
4. Network Measurements
5. Extract network statistics and connectivity matrices from network datatype