Hi Emily,
don't use .w files as they might generate a different number of data
points. The number of nodes is constant, but the .w file will attempt
to do a "compression" by eliminating nodes that are 0. This, of course,
turns into a bookkeeping mess, which is why I discourage the use of .w
files. Use mgh instead. You should then be able to use mris_convert to
convert to ascii, something like:
mris_convert -c your.mgh lh.white your.asc
doug
Emily Cooper wrote:
Dear FreeSurfer
gurus,
We are trying to conduct a simple group analysis, employing
freesurfer. However, our aim is to use the software only up to the
point where the functional data is projected to a common space, and
from that point on export the data to a text file and conduct the
analysis using an external mathematical package (R,
http://www.r-project.org).
We have received very useful information
from this message board in the last 2 weeks assisting us in this
endeavor, but are still stumped by part of the workflow.
At this point, we have succeeded in projecting our functional files
(AFNI format) to the FreeSurfer surface representation so that each
individual functional data is project to the individual registered
surface. Given that each individual surface has a different number of
surface
nodes, we reasoned that to conduct a group analysis, it would be
necessary to project the functional data not to the individual surface
of each participant, but instead, to the registered icosahedron
representation. The documentation of mri_vol2surf states that using the
"icoorder" option, will result in mapping to an icosahedron
with *prespecified* sizes. Specifically, we have tried projecting to
an ico with order 7 (documentation states 163842 nodes in this
reprsentation).
However, when using this option and
outputting to a "paint" (.w) file, we do not get this number of nodes
for the icosahedron. Instead, different subjects' icosahedrons have
different numbers of nodes. This is evident when the paint file is
converted to and ".asc" file via mris_convert. Before we continue, we
would like to know if this is a bug in mri_vol2surf, in mris_convert,
or perhaps not a bug at all (i.e., different icosahedrons may indeed
have different number of nodes by design).
Now that we find ourselves with no way to equate the number
of nodes in each participants' surface representation we are faced
with a quandary: How do we conduct the group analysis? It has been
suggested to us that we use the surf2surf utility. The documentation
of that utility mentions that both the src and target surfaces may be
icosahedrons. If we do indeed need to use this utility, should we map
data between icosahedrons, or would it be better to cut down one stage
of interpolation and just directly project the surfaces of all
subjects to one reference subject (
e.g., subject b -> subject a,
subject c ->subject a, and so on).
Thanks for any assistance,
Emily
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting