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Data: This pipeline accepts list of subjects with

• T1 anatomical NIFTI file,
• central surface file,
• list of label files to apply volume registration,
• list of "co-registered" multi modal volume images and
• list of vertex based text properties to generate GSBSS based mapping files.

Prerequisite MaCRUISE and SLANT pipeline Instructions at the bottom of the page

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File structure:

• INPUTS
  • subjlist.txt
  • TPM_template.nii – target MNI template
  • centralSurf_antsDeform.gii – target surface
  • subj1/
  • subj2/
  • subjn/

subjlist.txt name subj1 subj2 .. subjn

Each subject folder should have following files (Eg: for subj1)

• subj1
  • T1.nii.gz (Skull stripped)
  • insurface_0/ target_image_GMimg_centralSurf.asc
  • label_files_0/ --> label_1.nii.gz, ... label_i.nii.gz
  • volimages/ --> mod1_1.nii.gz, ... mod2_j.nii.gz
  • txt_files_0/ --> prop_1.txt, prop_k.txt
  • searchdir/ --> odi.nii.gz, viso.nii.gz

Dependencies:

• MaCRUISE pipeline to generate central surface and surface based properties (Eg: cortical thickness)

Following is the directory structure seen in OUTPUTS folder (Eg: subj1)

• OUTPUTS
  • subj1
    • regdir/
    • surfregdir/mappings.mat
    • outdir/ --> subj1_deformedMetrics.vtk
    • MAP_ALL/

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Prerequisite MaCRUISE surface

Full command to run macruise from command line

sudo docker run --rm -v /yourfolder/INPUTS/:/INPUTS/ -v /yourfolder/OUTPUTS/:/OUTPUTS/ vuiiscci/vuiiscci:MaCRUISE_v3_1_0 xvfb-run -a --server-args="-screen 0 1920x1200x24 -ac +extension GLX" /extra/MaCRUISE_v3_1_0

The INPUTS directory should have the following:

orig_target_seg.nii.gz T1.nii.gz

Prerequisite SLANT pipeline

Get the docker

sudo docker pull vuiiscci/slant:deep_brain_seg_v1_0_0

More details: https://github.com/MASILab/SLANTbrainSeg/

The INPUTS directory should have the following: T1.nii.gz