Index of /sereno/cereb/updates/vermis-labels

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cerebellar vermis labels/patches -- Dec 2024
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https://pages.ucsd.edu/~msereno/cereb/updates/vermis-labels/README.txt

These are new labels and surfaces for two very slightly different
revisions of the cerebellar surface.

The directory "cerebmap20" contains labels and surface patches compatible
with the dataset released with Sereno et al. (2020):

  rh-antvermis.label               -- anterior lobe vermis label
  rh-intvermis.label               -- cereb2c-export intermed vermis xfer2'd
  rh-postvermis.label              -- cereb2c-export posterior vermis xfer'd
  rh.smoothwm-antvermis.patch.3d   -- folded 3d patch of anterior lobe vermis
  rh.smoothwm-intvermis.patch.3d   -- folded 3d patch of intermediate vermis
  rh.smoothwm-postvermis.patch.3d  -- folded 3d patch of posterior vermis
  rh-vermislabel-smoothwm.tiff     -- image of all 3 labels
  rh-vermislabel-smoothwm-top.tiff -- image topview anterior lobe vermis label

The intermediate and posterior vermis labels were transferred from the
cereb2c-export surface (details below).  The binary freesurfer patch
files contain vertex numbers and folded surface coordinates (byteorder:
MSB first):

  -1 (4-byte int 'header')
  vtxcnt (4-byte int)
  vtx (4-byte int, N.B. 1-based, so subtract 1 !!!, negvtx=border)
  x (4-byte float)
  y (4-byte float)
  z (4-byte float)
  [etc: vtx,x,y,z, ...]

The directory "cereb2c-export" contains labels compatible with a slightly
earlier version of the released data:

  rh-antvermis.label               -- cerebmap20 label xfer'd to cereb2c-export
  rh-intvermis.label               -- intermediate vermis for cereb2c-export
  rh-postvermis.label              -- posterior vermis for cereb2c-export
  rh-vermislabel-smoothwm.tiff     -- image of all 3 labels

The first label here, rh-antvermis.label, is the cerebmap20
rh-antvermis.label (which will have vertex numbering for the distributed
cerebmap20 surface data), transferred to the earlier surface version,
cereb2c-export (which will have a different vertex numbering), using
the new csurf/tksurfer functions (read_label_to_nearest_annot_using_col
and fill_annot_holes_neigh):

  # pick foreign label (for different edit of same surface reconstruction)
  setfile label $env(SUBJECTS)/cerebmap20/label/rh-antvermis.label

  # read it into current surface and touch it up
  read_label_to_nearest_annot_using_col <r> <g> <b>
  fill_annot_holes_neigh 4 0.5

  # re-cut label and write it out into cereb2c-export label dir
  labeled_cut_clearvals 0              # re-cut current labeled
  setfile label ~/label/rh-antvermis.label
  write_val_visible_vertices

  # HOWTO touch up a few remaining holes
  [make everything-but-vermis label by FILL'ing around it]
  [read in everything-but-vermis label, FILL to get vermis]

The second label is the intermediate vermis label (not previously
published), which is situated in between the anterior and posterior
vermis labels.  The third label, rh-postvermis.label, is the posterior
vermis label for the earlier cereb2c-export surface version (which was
illustrated at the bottom of Fig. 2 of the 2020 paper).


SURFACE COORDINATE SYSTEM AND AREAL MEASUREMENTS

The voxels in the original 3D images are natively 0.19 x 0.19 x 0.19 mm.

However, in order to avoid downsampling the image data before making
surfaces from it, the data was imported into csurf as if it was a csurf
'conforming' 512^3 data set with 0.50 x 0.50 x 0.50 mm voxels, that
is, without resampling.  Therefore, the freesurfer 3D vertex mm
coordinates of the surfaces:

  rh.orig
  rh.smoothwm
  rh.inflated

are larger than actual size by a factor of 0.50/0.19.

A tksurfer tcl script, rescale2actual.tcl, is included to properly
scale down the surfaces, using a factor of 0.19/0.50 = 0.38, followed
by a 3% volume shrinkage correction (=1% linear), so that veridical
areal measurements can be made (e.g., using the FILL button in
tksurfer).

The script uses the following tksurfer tcl commands:

  really_scale_brain 0.38 0.38 0.38
  redraw
  really_scale_brain 1.01 1.01 1.01
  redraw
  setfile outsurf $insurf-actual
  write_binary_surface

N.B.: to rescale the flat surface patches, instead use:

  really_scale_brain 0.38 0.38 0.38
  redraw
  really_scale_brain 1.01 1.01 1.01
  redraw
  set origpatch $patch
  setfile patch $origpatch-actual
  write_binary_patch

For details of the original reconstruction, see:

  Sereno, M.I., J. Diedrichsen, M. Tachrount, G. Testa-Silva, H. d'Arceuil,
    and C. De Zeeuw (2020)
  The human cerebellum has almost 80% of the surface area of the neocortex.
  Proceedings of the National Academy of Sciences USA 117:19538-19543.
  https://pages.ucsd.edu/~msereno/papers/Cereb20.pdf
  https://pages.ucsd.edu/~msereno/papers/CerebSuppl20.pdf