I'm sorry that my message was confusing. The command line in your answer produces WM surface and thickness information per WM-vertex. I need thickness info per GM-vertex. So to say, the thickness 'below the surface' (because GM) and not above it (because WM). Since the number of vertices for the grey matter is somewhat greater than for the white in the same brain, it is necessary to map the 'thickness' to the pial surface. The command line I tried, is related to that question: mri_surf2surf --hemi lh ?srcsubject bert --srcsurfval lh.thickness --hemi lh --trgsubject bert --trgsurfval lh.pial --hemi lh
THX! Cheers Denny
Bruce Fischl wrote:
try doing:
mris_convert -c lh.thickness lh.white lh.thickness.asc
(note that this is in the mris_convert help)
cheers, Bruce
On Thu, 31 Dec 2009, Denny Milakara wrote:
yes, without any switch it is outputed with vertices and faces. The conversion to .off is trivial with matlab. If there is a need I can provide the code needed for conversion. I didn't though converted it from RAS to xyz, since it works well with MeshLab and RoffView in MSWindows.
I find it very interesting to include the cortical thickness information in surface information, ideally a thickness value per vortex. I found several postings about this issue, but I obviously didn't understand that process correctly.
If I try in 'bert/surf' this: mris_convert lh.thickness bert_thickL.asc I get this: Segmentation fault
So, I tried to map thickness to pial surface, by doing this: mri_surf2surf --hemi lh ?srcsubject bert --srcsurfval lh.thickness --hemi lh --trgsubject bert --trgsurfval lh.pial --hemi lh but I got that: ERROR: Option ?srcsubject unknown
What am I doing wrong?
Cheers, Denny
Bruce Fischl wrote:
no, and I don't think you should use -p. Try having the output be R.asc and see how it works (-p is to convert patches, and -c is for curvature files. The default is for surfaces)
cheers, Bruce
On Wed, 30 Dec 2009, Denny Milakara wrote:
yes, I also expected integers - indices of vertices that describe the faces (in this case triangular faces). I guess the following command produced the incomplete result: mris_convert -p rh.pial R.txt
Should I have used switch '-c'?
Bruce Fischl wrote:
the index is implicit by position (e.g. the first face is 0, the 2nd is 1, etc...). Each face just lists the vertices (by index) that are in it On Wed, 30 Dec 2009, Denny Milakara wrote:
Shouldn't the faces be integer numbers? There are no integers at the end of the output file. Is it possible to generate ASCII file without faces?
I need brain surface only, so I assume that 'lh.pial' and 'rh.pial' are OK for that purpose.
Cheers, Denny Milakara
Bruce Fischl wrote: > Hi Denny, > > the faces are in the 2nd half of the file. If you scroll (way) down > you'll find them. The columns are the x,y,z coords in what we call > surface RAS, which is documented on our wiki. > > cheers, > Bruce > > p.s. what surfaces you need are need is dependent on what you want to > do (e.g. inflated, white, etc...) > > On Wed, 30 Dec 2009, Denny Milakara wrote: > >> Thank you for your answer Bruce, >> >> >> Nobody expects here default solutions for exotic needs. So let me be >> more specific: >> >> I used 'mris_convert' to convert 'lh.pial' in ASCII format. The output >> file containes 3 colummns of real numbers with 3xwhitespace between >> them. >> >> 1) Are 'lh.pial' and 'rh.pial' the proper and only needed source files >> for converting and subsequent rendering of cortex surface? >> >> 2) Does each row contain x y z of vertices in RAS space? If not, what >> information then contain those columns? >> >> 3) I don't see the faces in the output file. How can I generate them? >> >> >> Regards, >> Denny Milakara >> >> >> >> Bruce Fischl wrote: >>> nothing by default that will do it, but it should be easy enough in >>> matlab >>> >>> >>> On Mon, 21 Dec 2009, Denny Milakara wrote: >>> >>>> Dear Freesurfers, >>>> >>>> >>>> I wonder if there is a way to output the triangulated pial surface >>>> for >>>> both hemispheres into a single ASCII file according to OFF-file >>>> schema: >>>> ---------------------------------- >>>> OFF numVertices numFaces numEdges >>>> x y z >>>> x y z >>>> ... numVertices like above >>>> NVertices v1 v2 v3 ... vN >>>> MVertices v1 v2 v3 ... vM >>>> ... numFaces like above >>>> --------------------------------- >>>> ...where the number of edges is to be ignored. >>>> >>>> >>>> Thank you for your suggestions! >>>> Denny Milakara >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >>