I've rigged the curv format reader to recognize volume files used to
encode surface values, so anything that accepts curv will also accept
mgh. The issue on the number of vertices is whether the rh.white is that
of the target subject used with mri_vol2surf. Are you using fsaverage?
doug
Emily Cooper wrote:
Hi Doug,
I tried commands like this one initially, originally getting a
"Segmentation fault" error. It was my understanding from the help file
that using the -c flag specified that I want to convert the curv file
to .asc. What I would like to do is convert a functional file to .asc.
A command like
mris_convert trim_action.100.int.surf.pfa10.forconvert.mgh
trim_action.100.int.lh.white.asc
inputing either an mgh in the subjects space or mapped to icosahedron
space gives that same error, which is why I switched to using .w as
input. However, including the -c flag gives a different error:
mris_convert -c trim_action.100.intval.ico7.mgh rh.white
trim_action.100.int.rh.white.asc
INFO: NOT fixing vertex area
ERROR: number of vertices in trim_action.100.intval.ico7.mgh does not
match surface (163842,156835)
maybe because functional data in the icosahedron space does not have
at .white file?
Emily
On 12/5/06, Doug Greve < [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
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 <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
[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
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
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
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
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