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Garikoitz Lerma-Usabiaga edited this page Nov 29, 2021 · 14 revisions

anatROIs (draft)

RTP2-anatROIs involves the processing of the subject’s anatomical T1w image, with the objective of obtaining the ROIs that will later be used in tractography (RTP-preproc and RTP-pipeline). The input of this step is the subject’s T1w file and ROIs defined in MNI space; the output is a segmented T1w image and ROIs of interest in individual subject T1w space. AnatROIs provides many predefined ROIs, and it is possible to extend it in multiple ways

Structural preprocessing and ROI creation

This container runs Freesurfer, and a set of other components to create ROIs.

Input

One of:

  1. T1 nifti image
  2. Already processed full freesurfer pipeline

Optional:

  1. Zip file containing volumetric ROIs in MNI: they will be converted to individual subject space
  2. Zip file containing surface ROIs in fsaverage: they will be converted to individual subject space

Output

Freesurfer's standard output + a folder with a set of ROIs. Most importantly, it will generate a file called fs.zip that is required as an input to RTP-pipeline. fs.zip can be created in this container, or if it is required (because we want to create the ROIs manually, for example) it can be created locally. The folder should contain a folder called fs/ in the base, and nothing else. In the fs folder there will be two things:

  1. brainmask.nii.gz, aparc+aseg.nii.gz (required) and other optional files.
  2. a folder called ROIs: in this folder all the binary nifti ROIs will be stored.

Main components of the container:

  1. Freesurfer 7.1.1 version (add link and citation)

  2. Tools to obtain ROIs (by segmentation or other means)see here

  3. Existing MNI atlases we already included in the tool: see here

  4. Hippocampal and Thalamic segmentation (add link and citation)

  5. Neuropythy (add link and citation)

  6. Cerebellum atlas (add link and citation)

  7. Mori atlas ROIs (add link and citation)

More documentation

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