All Pipelines

T1 Volumetric (FreeSurfer)

Available

This pipeline uses FreeSurfer's recon-all workflow to perform fully automated cortical surface reconstruction and volumetric parcellation from a T1-weighted structural MRI scan. Outputs include subject-specific cortical thickness maps, subcortical structure volumes, and a QC report with surface overlay images. Processing time is approximately 6–8 hours per subject on the local Linux worker.

Structural MRIT1wCortical ThicknessSegmentationFreeSurfer

Accepted Inputs

  • DICOM (.zip)
  • NIfTI (.nii, .nii.gz)

Expected Outputs

  • Volumetric masks (.mgz)
  • Regional volume metrics (.csv)
  • Cortical thickness maps
  • QC report (.html)

Technical Specifications

Worker Requirement
local-linux-freesurfer
Estimated Duration
~6–8 hours

References

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