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cerebellar dentate nucleus surfaces -- Apr 2025
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https://pages.ucsd.edu/~msereno/cereb/updates/dentate-nucleus/README.txt

The tarfile, cerebmap20-dentate.tgz, unpacks into a freesurfer subject
directory, cerebmap20-dentate, containing 3D images and surface data of
the left and right deep cerebellar dentate nucleus in the same coordinate
system as the original cerebellar cortex reconstruction.

If you use this data, mention my name and include this URL reference to its
source:

  https://pages.ucsd.edu/~msereno/cereb/updates/dentate-nucleus/

The files included are:

------------------------------------------------------------
+---cerebmap20-dentate
|   +---label
|   +---mri
|   |   +---orig
|   |   +---PD-flat.mgz
|   |   +---tmp
|   |   +---transforms
|   +---scripts
|   |   +---rescale2actual.tcl
|   |   +---NOTES
|   |   +---csurf.dat
|   +---surf
|   |   +---lh.orig
|   |   +---lh.smoothwm
|   |   +---lh.fullcut.patch.3d
|   |   +---lh.sulc
|   |   +---rh.orig
|   |   +---lh.curv
|   |   +---lh.full.patch.3d
|   |   +---rh.smoothwm
|   |   +---rh.inflated
|   |   +---lh.inflated
|   |   +---rh.full.patch.flat
|   |   +---rh.sulc
|   |   +---lh.fullcut.patch.flat
|   |   +---rh.fullcut.patch.3d
|   |   +---rh.full.patch.3d
|   |   +---lh.full.patch.flat
|   |   +---rh.fullcut.patch.flat
|   |   +---rh.curv
|   +---tmp
------------------------------------------------------------

N.B.: The surface prefixes are "rh/lh", but the surfaces only include
the deep cerebellar dentate nuclei.


SURFACE FORMAT AND SIZE

The surfaces are standard binary FreeSurfer triangle format, arranged
in a standard FreeSurfer subject directory that can be efficiently
displayed with csurf tksurfer.  You can download csurf for Mac or
Linux from here:

  https://pages.ucsd.edu/~msereno/csurf
           *or*
  https://mri.sdsu.edu/sereno/csurf

N.B.: The 512^3 volume images cannot be loaded by MGH FreeSurfer freeview.
Also, note that MGH FreeSurfer 7.1 no longer includes tkmedit and
tksurfer.  Also FreeSurfer 5.3 no longer works on MacOS 10.15 (Catalina).
However, csurf tkmedit and tksurfer *do* work on Catalina 10.15 (and on
all Mac OS from 10.6 (Snow Leopard) to current :-} ).

Once a surface has been opened in csurf tksurfer, it can be exported
to a number of other surface formats by using the larger [fn]-F3
interface and one of the following buttons on the "outsurf:" line:

  W	native freesurfer format (binary)
  ASC	freesurfer format (ASCII)
  VTK	vtk 3.0 format (ASCII)
  OFF	object file format: OFF,COFF (ASCII)
  STL	stereolithography format: 3D printer (ASCII)
  GLB	glTF 2.0: GL transmission format (binary)
  OBJ	Alias/Wavefront (ASCII)


SURFACE COORDINATE SYSTEM AND AREAL MEASUREMENTS

The voxels in the 3D image:

  PD-flat.mgz

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, it 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

Note that the scaling operation misaligns the rescaled surface with
respect to the (included) unscaled 3D image from which it was made.