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.whitetrim_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 greve@nmr.mgh.harvard.edu 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). 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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