Index of /sereno/cereb/data

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cerebmap20 -- 19 July 2020
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The tarfile, cerebmap20.tgz, unpacks into a freesurfer subject
directory, cerebmap20, containing 3D image and surface data that
was used in the paper:

  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.

The files included are:

------------------------------------------------------------
+---cerebmap20
|   +---mri
|   |   +---filled.mgz
|   |   +---orig.mgz
|   |   +---PD.mgz
|   |   +---T2.mgz
|   |   +---wm.mgz
|   +---scripts
|   |   +---NOTES
|   |   +---README.txt
|   |   +---rescale2actual.tcl
|   +---surf
|   |   +---rh.area
|   |   +---rh.curv
|   |   +---rh.inflated
|   |   +---rh.orig
|   |   +---rh.pial
|   |   +---rh.pial-actual.patch.3d
|   |   +---rh.sulc
|   |   +---rh.white
|   +---tmp
------------------------------------------------------------

N.B.: The surface prefixes are "rh", but the surface extends across
both hemispheres of the cerebellum.


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:

  http://www.cogsci.ucsd.edu/~sereno/.tmp/dist/csurf
           *or*
  https://mri.sdsu.edu/sereno/csurf

N.B.: These surfaces are very large (4.6M vertices, 9.2M triangles).
They are about 25x the size of a standard freesurfer cortical
hemisphere.  Because of this, they will take a while to load (about
12 seconds to load in csurf tksurfer; but about 2 minutes to load
in FreeSurfer 5.3 freeview).  These surfaces can't be loaded by
FreeSurfer 5.3 tksurfer (too large).  Also, it's best to have at
least 16G of RAM to avoid slowdown during surface loading due to
swapping.

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
(and FreeSurfer 5.3 no longer work on MacOS 10.15 Catalina).  However,
csurf tkmedit and tksurfer *do* work on Catalina :-} ).

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 all the 3D images:

  T2.mgz    
  PD.mgz
  orig.mgz
  wm.mgz
  filled.mgz

are natively 0.19 x 0.19 x 0.19 mm.

However, in order to avoid downsampling the image data before making
a surface 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.white
  rh.pial
  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

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


CEREBELLAR CORTEX-ONLY PATCH

A properly scaled and shrinkage-corrected 3d patch containing only
the cerebellar cortex is included.  To view this, first load any
surface, then read the patch:

  rh.pial-actual.patch.3d

using the "R" button on the "patch:" line in tksurfer.  This 3D
patch can be used for areal measurements using the tksurfer FILL
button (with many seeds, takes ~1 min).

To see what this patch looks like on the inflated surface, first
open the inflated surface, then click the "M" (mask) button on the
"patch:" line (entry should have auto-loaded rh.pial-actual.patch.3d)
to only show vertices from the inflated surface that are in the
patch (N.B.: the inflated surface has not been rescaled).

To make sense of the resulting image, which includes the flocculus
and the vermis, you can turn on the lighting for the inside of the
surface using:

  ctrl-middle-click-REDRAW


SPHERICAL MORPH

A spherical morphing of the surface of this cerebellar reconstruction
is available here:

  https://drive.google.com/drive/folders/1LXzFAsrWls2MoECl2yIKA-2WKv8_UJVO

Note that the representation of the original local surface area is
*extremely* distorted in the spherical morph because of the large and
locally variable amount of intrinsic (Gaussian) curvature.