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anatROIs

RTP2-anatROIs processes the subject’s anatomical T1w nifti image to obtain ROIs that will later be used in tractography (RTP-preproc and RTP-pipeline). The input of this step is the subject’s T1w file (native space) 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.

If starting with DICOM files (directly from the scanner), HeuDiConv can be used to convert the DICOMs to nifti files and transform them into BIDS format (Gorgolewski et al., 2016).

Structural preprocessing and ROI creation

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

Main components of the container:

1. Freesurfer 7.3.2
2. Tools to obtain ROIs (by segmentation or other means) [see here]
3. Existing MNI atlases we already included in the tool [see here]

Inputs

One of either:

1. T1 nifti image
   -or-
2. Already processed full freesurfer pipeline (zipped)

Optional (if the folder and file are there, the container will use them):

• Zip file containing volumetric ROIs in MNI: they will be converted to individual subject space
  -or-
• Zip file containing surface ROIs in fsaverage (annotations): they will be converted to individual subject space

Outputs

1. Recon-all standard output
2. fs.zip (this will be used for RTP-pipeline)
3. Others

More documentation

• Installation
• How to use
• Reporting and citation In this wiki page we include examples of how to report and cite RTP and all the included tools, it will change depending on the selected tools.
• TO-DO list