Freesurfer Processing Steps

Freesurfer Processing Steps

recon-all -i <structural1.nii> -autorecon1 -s <subj>

This will convert the structural images into FS-compatible files stored in {subjectdir}/scotty/mri/001.mgz Multiple structaral images will be combined if more than one -i flag is sent Then registers, averages over set, normalizes intensity etc, and skull strip check:

registration: tkregister2 --mgz --s <subj> --fstal strip and normalize: tkmedit scotty brainmask.mgz -aux T1.mgz recon-all -autorecon2 -s <subj> recon-all -subcortseg -s <subj> Subcortical and cortical volume segmentation recon-all -segmentation -s <subj> white/gray matter segmentation recon-all -autorecon2-wm -s <subj> or recon-all -autorecon2-pm -s <subj> generates white and pial surfaces (or regenerates pial with -pm flag) check:

tkmedit <subj> brainmask.mgz lh.white -aux wm.mgz -aux-surface rh.white

tk <subj> lh inflated recon-all -autorecon3 -s <subj> Spherical registration and parcellation check:

tksurfer <subj> lh smooth (or inflated, white, pial, orig, sphere) Load curvature lh.curv

Load label annotations lh.aparc.annot

Flattening

Make relaxation cuts

tksurfer <subj> lh inflated

Load curvature file lh.curv

Cut along calcarine by clicking then select cut

Cut through sylvian, 3 radial cuts along medial wall

Cut along calcarine beginning at pole: click, then select cut Excise medial wall by circling, click Cut Closed Line, then select exterior and Fill Uncut Area Click three times (along central sulcus?) to define plane to segment occip surface, then fourth on occip surface Click cutplane Make sure temporal pole is cut off save patch as <hem>.occip.patch.3d For full surface: Remove medial wall by circling, clicking Cut Closed Line, click on circle and then Fill Uncut Area Save patch lh.full.patch.3d Repeat with rh cd to <subj> flatten

calls mris_flatten -w 10 lh.occip.patch.3d

lh.occip.patch.flat for each hem

Processes: call recon-all command -s <subj>

-autorecon1 1. Motion Correction and Conform 5 min 2. NU (Non-Uniform intensity normalization) 3 min 3. Talairach transform computation 1 min 4. Intensity Normalization 1 3 min 5. Skull Strip 1 min 6. EM Register (linear volumetric registration) 8 min -autorecon2

-subcortseg

7. CA Intensity Normalization 1 min

8. CA Non-linear Volumetric Registration 10 hours

9. Remove Neck 3 min

10. LTA with Skull 9 min

11. CA Label (Volumetric Labeling) and Statistics 30 min

-segmentation or -autorecon2-cp to continue through

0. Intensity Normalization 2 (start here for control points) 3 min

1. White matter segmentation 4 min

2. Edit WM With ASeg 1 min

-autorecon2-wm to continue through

0. Fill (start here for wm edits) 1 min

1. Tessellation (begins per-hemisphere operations) 1 min/h

2. Smooth1 1 min/h

3. Inflate1 1 min/h

4. QSphere 16 min/h

5. Automatic Topology Fixer (recon-all -fix -s scotty) 1-9 hours/h -autorecon2-pm to finish

0. Final Surfs (start here for brain edits for pial surf) 1-2 hours/h

1. Smooth2 1 min/h

2. Inflate2 2 min/h

3. Cortical Ribbon Mask 1 min/h

-autorecon3

25. Spherical Mapping 1-2 hours/h

26. Spherical Registration 1 hour/h

27. Spherical Registration, Contralateral hemisphere 1 hour/h

28. Map average curvature to subject 1 min/h

29. Cortical Parcellation - Desikan_Killiany and Christophe (Labeling) 1 min/h

30. Cortical Parcellation Statistics 1 min/h

31. 1 min/h

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