if you convert the ?h.orig file as well as the patch, it will contain the coordinates of that surface. You'll need to convert them to voxel indices from RAS coords, but that's pretty straightforward. Your question is a bit confusing though, as the surface is a 2D manifold embedded in the 3D volume, so for example, all the orig coordinates will be on voxel boundaries (i.e. all the coordinates will end in .5). What are you trying to do?
Does that answer your question? Bruce On Thu, 1 Nov 2001, Claus Tempelmann wrote: > Hi Bruce again, > > thanks for your patience! May be I got it, if I did there was probably > a misunderstanding, I'm not looking for the 3D coordinates for the orig > or white or pial surface, but the coordinates of the corresponding > voxels in the original anatomical data, i.e. I want to know which voxels > in which of the files > COR-001 to COR-256 in the directory /subject/mri/orig belong to my patch. > Can I derive this information from the asc-files created with mris_convert? > > Claus > > > > > From [EMAIL PROTECTED] Thu Nov 01 20:59:44 2001 > > Envelope-to: [EMAIL PROTECTED] > > Delivery-date: Thu, 01 Nov 2001 20:59:44 +0100 > > X-Authentication-Warning: surfer.nmr.mgh.harvard.edu: majordomo set sender to >[EMAIL PROTECTED] using -f > > Date: Thu, 1 Nov 2001 14:56:56 -0500 (EST) > > From: Bruce Fischl <[EMAIL PROTECTED]> > > To: <[EMAIL PROTECTED]> > > Subject: Re: from flat map to origs > > MIME-Version: 1.0 > > > > Hi Claus, > > > > the coordinates are in the flat space, in which z=0 for all vertices. The > > last number is the vertex index, which is invariant across surface > > representations. You can therefore convert the orig (or white or pial) to > > ascii format and use the vertex index to lookup the 3D coordinate of that > > vertex on any of the surface representations. > > > > cheers, > > Bruce > > > > On Thu, 1 Nov > > 2001, Claus Tempelmann wrote: > > > > > Ok Bruce, > > > > > > mris_convert has worked, but I have no idea what the numbers in the asc-file > > > might mean. Is there a chapter in one of the manuals which would tell me > > > about it? > > > > > > I did the mris_convert with the complete rh.occip.patch.flat which is > > > not what I want but I assume it should work in the same way. Of course > > > I get a long file, about 40% of the file contains float coordinates > > > where the third coordinate is always 0.000000, > > > e.g. 9.62000 -37.419998 0.000000 > > > the rest of the file has three integer coordinates for each voxel (??) > > > but the numbers have up to 6 digits, > > > e.g. 146214 146207 144544 ?! > > > > > > If these are the voxel coordinates, which coordinate system is this? > > > > > > Claus > > > > > > > > > > > > > From [EMAIL PROTECTED] Thu Nov 01 20:19:40 2001 > > > > Envelope-to: [EMAIL PROTECTED] > > > > Delivery-date: Thu, 01 Nov 2001 20:19:40 +0100 > > > > X-Authentication-Warning: surfer.nmr.mgh.harvard.edu: majordomo set sender to >[EMAIL PROTECTED] using -f > > > > Date: Thu, 1 Nov 2001 14:17:19 -0500 (EST) > > > > From: Bruce Fischl <[EMAIL PROTECTED]> > > > > To: <[EMAIL PROTECTED]> > > > > Subject: Re: from flat map to origs > > > > MIME-Version: 1.0 > > > > > > > > Hi Claus, > > > > > > > > my mistake, I meant mris_convert, not mri_convert (since of course we are > > > > talking about surfaces not volumes). > > > > > > > > cheers, > > > > Bruce > > > > > > > > On Thu, 1 Nov 2001, Claus Tempelmann > > > > wrote: > > > > > > > > > Dear Bruce, > > > > > > > > > > thanks for the prompt reply. Doesn't sound too complicated :-) > > > > > However, all my old versions of mri_convert give the reply > > > > > unknown option -p > > > > > I am trying to get the October 2001 version downloaded, unfortunately > > > > > the connection isn't good enough for new speed records, anyway > > > > > finally I will get it. Hopefully that version knows about the > > > > > option -p ;-) > > > > > > > > > > Claus > > > > > > > > > > > > > > > > From [EMAIL PROTECTED] Thu Nov 01 19:20:14 2001 > > > > > > Envelope-to: [EMAIL PROTECTED] > > > > > > Delivery-date: Thu, 01 Nov 2001 19:20:14 +0100 > > > > > > X-Authentication-Warning: surfer.nmr.mgh.harvard.edu: majordomo set sender >to [EMAIL PROTECTED] using -f > > > > > > Date: Thu, 1 Nov 2001 13:17:39 -0500 (EST) > > > > > > From: Bruce Fischl <[EMAIL PROTECTED]> > > > > > > To: <[EMAIL PROTECTED]> > > > > > > Subject: Re: from flat map to origs > > > > > > MIME-Version: 1.0 > > > > > > > > > > > > Hi Claus, > > > > > > > > > > > > you should be able to use mri_convert -p <input patch> <output patch.asc) > > > > > > to convert a patch to ascii format, and therefore get the voxel coords out > > > > > > in matlab or whatever. > > > > > > > > > > > > cheers, > > > > > > Bruce > > > > > > > > > > > > On Thu, 1 Nov 2001, Claus Tempelmann wrote: > > > > > > > > > > > > > Hi everybody, > > > > > > > > > > > > > > many people are working with retinotopic maps on flat brains. > > > > > > > A typical task would be to identify a region on the flat map > > > > > > > (e.g. V2) and to get a list of all corresponding voxels of the > > > > > > > anatomical data set (e.g. 3D-scan). I assume some of you have already > > > > > > > done that with freesurfer tools. I would appreciate if you > > > > > > > could list the important steps on this way. > > > > > > > > > > > > > > Thanks in advance > > > > > > > > > > > > > > Claus > > > > > > > ------------------------------------------------------------------------- > > > > > > > Claus Tempelmann email: [EMAIL PROTECTED] > > > > > > > Clinic for Neurology II > > > > > > > MR department phone: +49-391-6117177 > > > > > > > OvG University Magdeburg +49-391-6117183 > > > > > > > Leipziger Strasse 44 > > > > > > > 39120 Magdeburg fax: +49-391-6117178 > > > > > > > Germany > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >
