information is very old...most machines where this stuff were
installed are gone...still, it is a lot of information, so I'd hate
to just delete it when it might be useful to someone, somewhere.
Dianne Patterson 10/25/2006
runs as a standalone program under MSWindows. MrFlatMesh contains
a series of Matlab routines and will run on any machine that has
allows one to classify voxels in a brain image into white matter
and CSF (using a combination of automatic and manual techniques
described in the tutorial) and then "grow" a gray matter
layer, to a specified thickness, on the white matter. This gray
matter can be saved as a 3d mesh file. MrFlatMesh uses the 3d mesh
file generated by mrGray as input for its unfolding operations.
NOTE: At this time (12/28/2001) , the software to view unfolded
maps or activations on those unfolded maps is not available.
we have several useful downloads:
MrGray Tutorial (word document; still under revision, but
useful, I hope)
(three flavors; this converts functional data from spm into a
functional overlay file that MrGray can read)
(This spm routine will read the mat file associated with an image
and actually flip the image into the described orientation. This
is crucial if you want to export an spm image to be read by another
program (like MrGray or MRIcro). It also reslices the image into
isotropic 1x1x1 voxels. If you get MakeMrGrayfun.m, then you'll
need John Ashburner's reorient.m)
can use MRIcro (a stand alone PC program) to create an "Analyze
format" image from your raw images (spm uses Analyze format,
so any spm image volumes will work).
you need to reorient the image volume you may use MRIcro's "save
as" utility. However, if you have nonisotropic voxels, this
may result in distortion. In such a case, John Ashburner's reorient.m
will use the *.mat file that spm generates to actually reorient
the image AND, it will slice the entire image into isotropic 1mm
x 1mm x 1mm voxels. Reorient.m requires Matlab and SPM to be installed.
you have the Analyze/SPM format *.img and *.hdr files, you can use
the Matlab routine (analyze2mrgray.m) provided with the conversion
utilities to create the correct 8 bit *.dat file used by mrGray.
For example, if you have an 8 or 16 bit image (fred.hdr and fred.img),
then the following matlab command will create a *.dat file (only
one) and allow you to name it:
program will convert 8 or 16 bit images to the correct format. It
will assume the images are 8 or 16 bit big-endian unless you tell
it to expect little endian. Analyze2mrGray uses routines that come
with mrFlatMesh and the SPM99 spm_vol command to parse the header.
It requires Matlab. Alternatively, MRIcro can convert the image
from 16 to 8 bit, using the "Save As" function.
Mr. Gray Fun
the tutorial document listed above to learn more about the format
of functional overlay files in MrGray. The three MakeMrgrayFun m-files
are all slightly different. All of them depend on Matlab, SPM and
Flip the 3D image to put it in
the same orientation as the functionals.
Apply reorient.m to the 3D structural after you have flipped it.
Coregister your functional images to the 3d structural image resulting
The rest of the functionals
direction of coregistration is important because you want a pristine
3D file with no attached mat file that might describe additional
orientation changes. The functionals will end up with the mat files.
Generate a write filtered image of the activations from the SPM
Results (after displaying the results of your analysis in SPM, select
"write filtered" and name the output file. We will call
this output file "activity".
ways to Make Mr. Gray Fun
apply reorient.m to activity.img:
will create ractivity.img)
will present an SPM gui interface for you to find and select "ractivity".
The program will produce an output called, in this case, ractivity.fun.
The result will map all activations into 4 levels of color). The
output is a text file which you can open and examine.
is like makemrGrayFun except that it will print 6 columns of voxel
coordinates. The first three columns are x,y and z in SPM. The next
three columns are the x,y,z coordinates in Mrgray. This allows one
to check the output and it allows one to generate a text file of
all the suprathreshold voxels in SPM.
This does not require the user to apply reorient.m to the activity.img.
In fact, it will probably run out of memory and bomb if you do apply
reorient.m to the activity file, because the underlying algorithm
is not very efficient. makeMrGrayFun1 asks the user to identify
both the activity file and the 3D anatomical. It then maps from
the native voxel space of the functional image to the voxel space
of the coregistered 3D image. An interesting side effect of this
is that the program will choose only one voxel in the 3D image to
represent each voxel in the functional image and thus generate far
fewer activations in the text file. The visual effect of this is
that the activations appear much smaller when displayed on the 3D
we prefer makeMrGrayFun.m, but the other two may have interesting
applications and are thus made available.