Beauchamp:FSAverageReadme

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This is the FreeSurfer group average subject.

DO NOT EDIT OR MODIFY THIS SUBJECT!

The surfaces were constructed from 40 subjects resmapled to a 7th order icosahedron using make_average_subject. See scripts/make_average_{surface,volume}.log for more info. It is similar to the old "average7", except that average7 did not retain information about the surface areas of the original subjects, so it was difficult to relate the metric properties (eg, cluster surface area) of average7 to that of a typical subject.

The annotations in the label dir are those from the probabilistic atlases, ie, curvature.buckner40.filled.desikan_killiany.gcs for ?h.aparc.annot, and atlas2005_simple.gcs for ?h.aparc.a2005s. The individual labels for each of these were extracted and placed in the label directory:

cd label mri_annotation2label --subject fsaverage --hemi lh \

 --annotation aparc \
 --table aparc.annot.ctab \
 --outdir .

mri_annotation2label --subject fsaverage --hemi rh \

 --annotation aparc \
 --table aparc.annot.ctab \
 --outdir .

mri_annotation2label --subject fsaverage --hemi lh \

 --annotation aparc.a2005s \
 --table aparc.atlas2005_simple.ctab \
 --outdir .

mri_annotation2label --subject fsaverage --hemi rh \

 --annotation aparc.a2005s \
 --table aparc.atlas2005_simple.ctab \
 --outdir .


The volumes were derived from the MNI305 (www.bic.mni.mcgill.ca). See also the mni305.cor.readme file. The MNI305 is the target for linear talairaching (more on this below). orig.mgz and T1.mgz are linked to mni305.cor.mgz. brainmask.mgz is linked to mni305.mask.cor.mgz. brain.mgz was created with mri_mask. The full volume creation process is:

cp $FREESURFER_HOME/average/mni305.cor.mgz . cp $FREESURFER_HOME/average/mni305.mask.cor.mgz . cp $FREESURFER_HOME/average/mni305.cor.readme . mri_add_xform_to_header -c auto mni305.cor.mgz mri_add_xform_to_header -c auto mni305.mask.cor.mgz ln -s mni305.cor.mgz orig.mgz ln -s mni305.cor.mgz T1.mgz ln -s mni305.mask.cor.mgz brainmask.mgz mri_mask T1.mgz brainmask.mgz brain.mgz

The volumes orig.group.mgz, T1.group.mgz, and brain.group.mgz were those originally produced by make_average_subject.

As mentioned above, the MNI305 is the target for linear talairaching. All volumes and surfaces are aligned to this brain.

This has several implications:

 1. The mri/talairach.xfm is identity
 2. tkregister2 --fstal --s fsaverage will bring up the same volume
    for movable and target.
 3. The surfaces coordinates are in talairach space, so they align
    with the MNI305 volume, so "tkmedit fsaverage T1.mgz lh.white",
    shows the surfaces overlaid properly on the brain.
 4. The c_{ras} for all volumes is 0. If you don't know what this
    means, consider yourself lucky.
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