hi doug, the target subject of mri_vol2surf was ico7 when i got the error in mris_convert. i tried using the command you gave when the target was the individuals sphere.reg, and got a text file with 5 columns. is the last column the intensity values? is there a way to use this command on data mapped onto ico7?
emily On 12/5/06, Doug Greve <[EMAIL PROTECTED]> wrote:
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.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 < [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). 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 > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > 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 > > -- 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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
