9. Sulci Reconstruction and Identification

9.1. Introduction

Preprocessing of functional MRI (fMRI) data is a crucial step in transforming raw scanner outputs into signals that can be meaningfully interpreted and compared across individuals. Raw fMRI volumes contain a variety of artifacts and sources of variability—such as head motion, scanner drift, geometric distortions, and physiological noise—that can obscure the underlying neural activity of interest. A standardized preprocessing workflow addresses these issues by aligning images across time and space, correcting for distortions, removing nuisance signals, and generating anatomically and functionally consistent representations of the data.

9.2. Requirements

CPU	RAM
1	1 GB

9.3. Description

Processing Steps

This analysis relies on morphologist’s pipeline [1].

• Automate High‑Quality Brain Segmentation The preprocessing performs full anatomical segmentation of T1 MRI data, including gray matter, white matter, and cerebrospinal fluid. This provides the foundation for downstream morphometric analyses.

• Extract and Analyze Cortical Surfaces The tool reconstructs cortical surfaces and generates meshes.

• Perform Detailed Sulcal Morphometry The sulcal analysis, includes sulcus recognition (now CNN‑based), sulcal depth, length, and span, gyrification index, and cortical fold graph construction.

Quality Control:

• Sulcal Morphometry scores Images were classified as motion outliers when they exceeded established thresholds for these metrics. Specifically, any volume with a mean framewise displacement greater than 0.2 mm, or with a mean standardized DVARS value exceeding 1.5, was flagged as low‑quality.

• Manual inspection Subject‑level quality‑control HTML reports are reviewed manually to ensure that preprocessing outcomes are consistent across participants and that no systematic artifacts remain.

9.4. Outputs

The sulcirec directory contains subject-level results, logs, and quality-control outputs. The structure is organized following the brainprep ontology.

sulcirec/
├── dataset_description.json
└── subjects
    └── sub-01
        └── ses-00
            ├── log
            │   └── report_20260409_112204.rst
            └── run-28236
                ├── anat
                │   ├── folds
                │   │   └── 3.1
                │   │       ├── sub-01_ses-00_run-28236_hemi-L.arg
                │   │       ├── sub-01_ses-00_run-28236_hemi-L.data
                │   │       │   ├── aims_Tmtktri.gii
                │   │       │   ├── bottom_Bucket.bck
                │   │       │   ├── cortical_Bucket.bck
                │   │       │   ├── junction_Bucket.bck
                │   │       │   ├── other_Bucket.bck
                │   │       │   ├── plidepassage_Bucket.bck
                │   │       │   └── ss_Bucket.bck
                │   │       ├── sub-01_ses-00_run-28236_hemi-L_sulcivoronoi.nii.gz
                │   │       ├── sub-01_ses-00_run-28236_hemi-R.arg
                │   │       ├── sub-01_ses-00_run-28236_hemi-R.data
                │   │       │   ├── aims_Tmtktri.gii
                │   │       │   ├── bottom_Bucket.bck
                │   │       │   ├── cortical_Bucket.bck
                │   │       │   ├── junction_Bucket.bck
                │   │       │   ├── other_Bucket.bck
                │   │       │   ├── plidepassage_Bucket.bck
                │   │       │   └── ss_Bucket.bck
                │   │       ├── sub-01_ses-00_run-28236_hemi-R_sulcivoronoi.nii.gz
                │   │       └── sul-0_auto
                │   │           ├── sub-01_ses-00_run-28236_sul-0_auto_sulcal_morphometry.csv
                │   │           ├── sub-01_ses-00_run-28236_sul-0_hemi-L_auto.arg
                │   │           ├── sub-01_ses-00_run-28236_sul-0_hemi-L_auto.data
                │   │           │   ├── aims_Tmtktri.gii
                │   │           │   ├── bottom_Bucket.bck
                │   │           │   ├── cortical_Bucket.bck
                │   │           │   ├── junction_Bucket.bck
                │   │           │   ├── other_Bucket.bck
                │   │           │   ├── plidepassage_Bucket.bck
                │   │           │   ├── ss_Bucket.bck
                │   │           ├── sub-01_ses-00_run-28236_sul-0_hemi-R_auto.arg
                │   │           └── sub-01_ses-00_run-28236_sul-0_hemi-R_auto.data
                │   │               ├── aims_Tmtktri.gii
                │   │               ├── bottom_Bucket.bck
                │   │               ├── cortical_Bucket.bck
                │   │               ├── junction_Bucket.bck
                │   │               ├── other_Bucket.bck
                │   │               ├── plidepassage_Bucket.bck
                │   │               └── ss_Bucket.bck
                │   ├── mesh
                │   │   ├── sub-01_ses-00_run-28236_head.surf.gii
                │   │   ├── sub-01_ses-00_run-28236_hemi-L_pial.surf.gii
                │   │   ├── sub-01_ses-00_run-28236_hemi-L_white.surf.gii
                │   │   ├── sub-01_ses-00_run-28236_hemi-R_pial.surf.gii
                │   │   └── sub-01_ses-00_run-28236_hemi-R_white.surf.gii
                │   ├── segmentation
                │   │   ├── sub-01_ses-00_run-28236_brain.nii.gz
                │   │   ├── sub-01_ses-00_run-28236_edges.nii.gz
                │   │   ├── sub-01_ses-00_run-28236_hemi-L_cortex.nii.gz
                │   │   ├── sub-01_ses-00_run-28236_hemi-L_csf.nii.gz
                │   │   ├── sub-01_ses-00_run-28236_hemi-L_grey_white.nii.gz
                │   │   ├── sub-01_ses-00_run-28236_hemi-L_gw_interface.nii.gz
                │   │   ├── sub-01_ses-00_run-28236_hemi-L_roots.nii.gz
                │   │   ├── sub-01_ses-00_run-28236_hemi-L_skeleton.nii.gz
                │   │   ├── sub-01_ses-00_run-28236_hemi-R_cortex.nii.gz
                │   │   ├── sub-01_ses-00_run-28236_hemi-R_csf.nii.gz
                │   │   ├── sub-01_ses-00_run-28236_hemi-R_grey_white.nii.gz
                │   │   ├── sub-01_ses-00_run-28236_hemi-R_gw_interface.nii.gz
                │   │   ├── sub-01_ses-00_run-28236_hemi-R_roots.nii.gz
                │   │   ├── sub-01_ses-00_run-28236_hemi-R_skeleton.nii.gz
                │   │   ├── sub-01_ses-00_run-28236_hfiltered.nii.gz
                │   │   ├── sub-01_ses-00_run-28236_nobias.han
                │   │   ├── sub-01_ses-00_run-28236_nobias.his
                │   │   ├── sub-01_ses-00_run-28236_nobias.nii.gz
                │   │   ├── sub-01_ses-00_run-28236_skull_stripped.nii.gz
                │   │   ├── sub-01_ses-00_run-28236_sul-0_brain_volumes.csv
                │   │   ├── sub-01_ses-00_run-28236_variance.nii.gz
                │   │   ├── sub-01_ses-00_run-28236_voronoi.nii.gz
                │   │   └── sub-01_ses-00_run-28236_whiteridge.nii.gz
                │   ├── sub-01_ses-00_run-28236_sul-0_morphologist_report.json
                │   ├── sub-01_ses-00_run-28236_sul-0_morphologist_report.pdf
                ├── qc.tsv
                ├── registration
                │   ├── sub-01_ses-00_run-28236_T1w.referential
                │   ├── sub-01_ses-00_run-28236_T1w_TO_MNI152.trm
                │   └── sub-01_ses-00_run-28236_T1w_TO_Talairach-ACPC.trm
                ├── sub-01_ses-00_run-28236.APC
                ├── sub-01_ses-00_run-28236_desc-conform_T1w.nii.gz
                ├── sub-01_ses-00_run-28236_normalized_SPM.nii
                ├── sub-01_ses-00_run-28236_sn.mat
                └── sub-01_ses-00_run-28236_sn_pass1.mat

Description of contents:

• dataset_description.json Metadata describing the process, including versioning and processing information.

• log/report_<timestamp>.rst Contains group-level workflow steps and parameters.

• quality_check/motion_confounds.tsv Table containing the mean standardized DVARS and mean FD for each subject/session/run. The table includes a binary qc column indicating the quality control result.

• subjects/sub-<id>/ses-<id>/logs/report_<timestamp>.rst Contains subject-level workflow steps and parameters.

• subjects/sub-<id>/ses-<id>/run-<id> Standard morphologist folder structure (https://brainvisa.info/axon-6.0/en/processes/categories/morphologist/category_documentation.html).

9.5. Featured examples

Sulci reconstruction Pre-Processing

Explore how to perform this analysis.

../auto_examples/workflows/plot_sulcirec.html

9.6. References

[1]

C. Fischer, Grégory Operto, S. Laguitton, Matthieu Perrot, I. Denghien, and D. Rivière. Morphologist 2012: the new morphological pipeline of brainvisa. Proceedings of the 18th HBM Scientific Meeting, 2012.