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First, run: {{{ recon-all -autorecon1 -subjid <subject name> }}} ...to generate the mri/nu which the ASEG uses as input. Then, run: |
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The process flowchart below shows the various input and output files created along the way. |
[wiki:FreeSurferWorkFlows top] | [wiki:HistoricalReconstruction previous]
FreeSurfer Subcortical Segmentation
FreeSurfer now automatically runs automated labeling of the brain volume and this is included in all versions of the September 2005 release. In subcortical segmentation, each voxel in the normalized brain volume is assigned one of about 40 labels, including:
- Cerebral White Matter, Cerebral Cortex, Lateral Ventricle, Inferior Lateral Ventricle, Cerebellum White Matter, Cerebellum Cortex, Thalamus, Caudate, Putamen, Pallidum, Hippocampus, Amygdala, Lesion, Accumbens area, Vessel, Central Diencephalon, Third Ventricle, Fourth Ventricle, Brain Stem, Cerebrospinal Fluid
However, if you processed your anatomical data using previous versions, you can just run the subcortical segmentation separately if you wish to obtain the automated labels. The September 2005 release of FreeSurfer by default uses the automatically segmented brain volume (ASEG) to segment the white matter volume (WM). You will use the -noedit_wm_with_aseg flag to ensure that it preserves and uses the white matter volume (WM) edits that you made.
First, run:
recon-all -autorecon1 -subjid <subject name>
...to generate the mri/nu which the ASEG uses as input.
Then, run:
recon-all -autorecon2 -noedit_wm_with_aseg -keepwmedits -subjid <subject name>
The process flowchart below shows the various input and output files created along the way.
Process Flow
recon-all step |
Input |
Command Line |
Output |
["recon-all"] -autorecon1 -subjid subj |
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orig/001.mgz |
["mri_motion_correct2"] -i orig/001.mgz -i orig/002.mgz -o rawavg.mgz |
rawavg.mgz |
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orig/002.mgz |
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rawavg.mgz |
["mri_convert"] rawavg.mgz orig.mgz --conform |
orig.mgz |
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orig.mgz |
["mri_convert"] orig.mgz orig.mnc |
orig.mnc |
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orig.mnc |
(4 iterations of) ["nu_correct"] -clobber nu0.mnc nu1.mnc |
nu4.mnc |
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nu4.mnc |
["mri_convert"] nu4.mnc nu.mgz |
nu.mgz |
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nu.mgz |
["talairach2"] subjid -mgz |
transforms/talairach.xfm |
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nu.mgz |
["mri_normalize"] nu.mgz T1.mgz |
T1.mgz |
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T1.mgz |
["mri_watershed"] T1.mgz brain.mgz |
brain.mgz |
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Check skullstrip (brain.mgz), talairach (transforms/talairach.xfm), and normalization (brain.mgz or T1.mgz - mean wm voxel value = 110) |
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["recon-all"] -autorecon2 -no_edit_wm_with_aseg -keepwmedits -subjid subj |
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brain.mgz |
["mri_em_register"] -mask brain.mgz -p .5 -fsamples fsamples.mgz nu.mgz $GCA transforms/talairach.lta |
transforms/talairach.lta |
|
nu.mgz |
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brain.mgz |
["mri_ca_normalize"] -mask brain.mgz nu.mgz $GCA transforms/talairach.lta norm.mgz |
norm.mgz |
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nu.mgz |
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transforms/talairach.lta |
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brain.mgz |
["mri_ca_register"] -cross-sequence -mask brain.mgz -T transforms/talairach.lta norm.mgz $GCA transforms/talairach.m3z |
transforms/talairach.m3z |
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transforms/talairach.lta |
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norm.mgz |
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norm.mgz |
["mri_ca_label"] -cross-sequence norm.mgz transforms/talairach.m3z $GCA aseg.mgz |
aseg.mgz |
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transforms/talairach.m3z |
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brain.mgz |
["mri_normalize"] -mask brain.mgz nu.mgz T1.mgz |
T1.mgz |
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nu.mgz |
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T1.mgz |
["mri_mask"] T1.mgz brain.mgz brain.mgz |
brain.mgz |
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brain.mgz |
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brain.mgz |
["mri_segment"] brain.mgz wm.mgz |
wm.mgz |
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wm.mgz |
["mri_edit_wm_with_aseg"] wm.mgz aseg.mgz wm.mgz |
wm.mgz |
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aseg.mgz |