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
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
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
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.
- Are 'lh.pial' and 'rh.pial' the proper and only needed source files
for converting and subsequent rendering of cortex surface?
- Does each row contain x y z of vertices in RAS space? If not, what
information then contain those columns?
- 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
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.
- Are 'lh.pial' and 'rh.pial' the proper and only needed source files
for converting and subsequent rendering of cortex surface?
- Does each row contain x y z of vertices in RAS space? If not, what
information then contain those columns?
- 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
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.
- Are 'lh.pial' and 'rh.pial' the proper and only needed source files
for converting and subsequent rendering of cortex surface?
- Does each row contain x y z of vertices in RAS space? If not, what
information then contain those columns?
- 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
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.
- Are 'lh.pial' and 'rh.pial' the proper and only needed source files
for converting and subsequent rendering of cortex surface?
- Does each row contain x y z of vertices in RAS space? If not, what
information then contain those columns?
- 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
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.
- Are 'lh.pial' and 'rh.pial' the proper and only needed source files
for converting and subsequent rendering of cortex surface?
- Does each row contain x y z of vertices in RAS space? If not, what
information then contain those columns?
- 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
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.
- Are 'lh.pial' and 'rh.pial' the proper and only needed source files
for converting and subsequent rendering of cortex surface?
- Does each row contain x y z of vertices in RAS space? If not, what
information then contain those columns?
- 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
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 > > >
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 >> >> >>
Hi Denny,
the number of vertices for the pial surface should be identical to the # in the white surface. The thickness is a property of both surfaces, and can be associated with either.
cheers Bruce On Thu, 31 Dec 2009, Denny Milakara wrote:
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 >>> >>> >>>
Hi Doug,
I'm a bit confused because the thickness values from the thickness file is not identical to the euclidean distances I calculated myself. Calculated value is always a bit greater.
Example #1 Pial left: -16.679081 -87.523453 30.427801 Thickness left: 000 -16.95796 -85.12147 30.10204 2.06924 Thickness value from file: 2.06924 Thickness value calculated: 2.44
Example #2 Pial left: -17.137926 -87.548676 30.134594 Thickness left: 001 -17.27066 -85.21771 29.78851 2.13066 Thickness value from file: 2.13066 Thickness value calculated: 2.3603
If the thickness values from l/rh.thickness are correct and not the pure 3d euclidean distances, what factor makes the difference between them?
Cheers,
Denny
-----Ursprüngliche Nachricht----- Von: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 30. Dezember 2009 22:15 An: Milakara, Denny Cc: FreeSurfer Forum Betreff: Re: [Freesurfer] Pial surface of both hemispheres as specific ASCII output
Hi Denny,
the number of vertices for the pial surface should be identical to the # in the white surface. The thickness is a property of both surfaces, and can be associated with either.
cheers Bruce On Thu, 31 Dec 2009, Denny Milakara wrote:
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 >>>> >>>> >>>>
Hi Denny,
the thickness we use is the shortest distance to the white surface from each point on the pial surface averaged with the shortest distance to the pial surface from each point on the white surface.
cheers Bruce On Wed, 27 Jan 2010, Milakara, Denny wrote:
Hi Doug,
I'm a bit confused because the thickness values from the thickness file is not identical to the euclidean distances I calculated myself. Calculated value is always a bit greater.
Example #1 Pial left: -16.679081 -87.523453 30.427801 Thickness left: 000 -16.95796 -85.12147 30.10204 2.06924 Thickness value from file: 2.06924 Thickness value calculated: 2.44
Example #2 Pial left: -17.137926 -87.548676 30.134594 Thickness left: 001 -17.27066 -85.21771 29.78851 2.13066 Thickness value from file: 2.13066 Thickness value calculated: 2.3603
If the thickness values from l/rh.thickness are correct and not the pure 3d euclidean distances, what factor makes the difference between them?
Cheers,
Denny
-----Ursprüngliche Nachricht----- Von: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 30. Dezember 2009 22:15 An: Milakara, Denny Cc: FreeSurfer Forum Betreff: Re: [Freesurfer] Pial surface of both hemispheres as specific ASCII output
Hi Denny,
the number of vertices for the pial surface should be identical to the # in the white surface. The thickness is a property of both surfaces, and can be associated with either.
cheers Bruce On Thu, 31 Dec 2009, Denny Milakara wrote:
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 >>>>> >>>>> >>>>> >
How different is your method from using lines perpendicular to tangent planes touching both pial and white surface vertices?
Cheers, Denny
-----Ursprüngliche Nachricht----- Von: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 27. Januar 2010 01:36 An: Milakara, Denny Cc: FreeSurfer Forum Betreff: Re: [Freesurfer] Pial surface of both hemispheres as specific ASCII output
Hi Denny,
the thickness we use is the shortest distance to the white surface from each point on the pial surface averaged with the shortest distance to the pial surface from each point on the white surface.
cheers Bruce On Wed, 27 Jan 2010, Milakara, Denny wrote:
Hi Doug,
I'm a bit confused because the thickness values from the
thickness file is not identical to the euclidean distances I calculated myself. Calculated value is always a bit greater.
Example #1 Pial left: -16.679081 -87.523453 30.427801 Thickness left: 000 -16.95796 -85.12147
30.10204 2.06924
Thickness value from file: 2.06924 Thickness value calculated: 2.44
Example #2 Pial left: -17.137926 -87.548676 30.134594 Thickness left: 001 -17.27066 -85.21771
29.78851 2.13066
Thickness value from file: 2.13066 Thickness value
calculated: 2.3603
If the thickness values from l/rh.thickness are correct and
not the pure 3d euclidean distances, what factor makes the difference between them?
Cheers,
Denny
-----Ursprüngliche Nachricht----- Von: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 30. Dezember 2009 22:15 An: Milakara, Denny Cc: FreeSurfer Forum Betreff: Re: [Freesurfer] Pial surface of both hemispheres as specific ASCII output
Hi Denny,
the number of vertices for the pial surface should be identical to the # in the white surface. The thickness is a property of both surfaces, and can be associated with either.
cheers Bruce On Thu, 31 Dec 2009, Denny Milakara wrote:
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
>>>>>> >>>>>> >>>>>> >>
Hi Denny,
in general the lines won't be perpindicular to both tangent planes. Using the surface normal to compute thickness fails dramatically in some cases (which is why we don't use it). Consider a flat bottomed U for the pial surface with a larger flat bottomed U for the white surface. Near the edges of the larger (white) U the surface normal is parallel to the pial surface and hence never intersects it.
cheers, Bruce
On Wed, 27 Jan 2010, Milakara, Denny wrote:
How different is your method from using lines perpendicular to tangent planes touching both pial and white surface vertices?
Cheers, Denny
-----Ursprüngliche Nachricht----- Von: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 27. Januar 2010 01:36 An: Milakara, Denny Cc: FreeSurfer Forum Betreff: Re: [Freesurfer] Pial surface of both hemispheres as specific ASCII output
Hi Denny,
the thickness we use is the shortest distance to the white surface from each point on the pial surface averaged with the shortest distance to the pial surface from each point on the white surface.
cheers Bruce On Wed, 27 Jan 2010, Milakara, Denny wrote:
Hi Doug,
I'm a bit confused because the thickness values from the
thickness file is not identical to the euclidean distances I calculated myself. Calculated value is always a bit greater.
Example #1 Pial left: -16.679081 -87.523453 30.427801 Thickness left: 000 -16.95796 -85.12147
30.10204 2.06924
Thickness value from file: 2.06924 Thickness value calculated: 2.44
Example #2 Pial left: -17.137926 -87.548676 30.134594 Thickness left: 001 -17.27066 -85.21771
29.78851 2.13066
Thickness value from file: 2.13066 Thickness value
calculated: 2.3603
If the thickness values from l/rh.thickness are correct and
not the pure 3d euclidean distances, what factor makes the difference between them?
Cheers,
Denny
-----Ursprüngliche Nachricht----- Von: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 30. Dezember 2009 22:15 An: Milakara, Denny Cc: FreeSurfer Forum Betreff: Re: [Freesurfer] Pial surface of both hemispheres as specific ASCII output
Hi Denny,
the number of vertices for the pial surface should be identical to the # in the white surface. The thickness is a property of both surfaces, and can be associated with either.
cheers Bruce On Thu, 31 Dec 2009, Denny Milakara wrote:
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
>>>>>>> >>>>>>> >>>>>>> >>> > >
I see the point.
In the file with 183284 vertices there are 14 negative thickness values ranging between -0.0002 and -0.2413. How do you explain the negative thickness values, or in another words what should I do with them?
Cheers, Denny
-----Ursprüngliche Nachricht----- Von: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 27. Januar 2010 02:06 An: Milakara, Denny Cc: FreeSurfer Forum Betreff: Re: [Freesurfer] Pial surface of both hemispheres as specific ASCII output
Hi Denny,
in general the lines won't be perpindicular to both tangent planes. Using the surface normal to compute thickness fails dramatically in some cases (which is why we don't use it). Consider a flat bottomed U for the pial surface with a larger flat bottomed U for the white surface. Near the edges of the larger (white) U the surface normal is parallel to the pial surface and hence never intersects it.
cheers, Bruce
On Wed, 27 Jan 2010, Milakara, Denny wrote:
How different is your method from using lines perpendicular
to tangent planes touching both pial and white surface vertices?
Cheers, Denny
-----Ursprüngliche Nachricht----- Von: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 27. Januar 2010 01:36 An: Milakara, Denny Cc: FreeSurfer Forum Betreff: Re: [Freesurfer] Pial surface of both hemispheres as specific ASCII output
Hi Denny,
the thickness we use is the shortest distance to the white surface from each point on the pial surface averaged with the shortest distance to the pial surface from each point on the white surface.
cheers Bruce On Wed, 27 Jan 2010, Milakara, Denny wrote:
Hi Doug,
I'm a bit confused because the thickness values from the
thickness file is not identical to the euclidean distances I calculated myself. Calculated value is always a bit greater.
Example #1 Pial left: -16.679081 -87.523453 30.427801 Thickness left: 000 -16.95796 -85.12147
30.10204 2.06924
Thickness value from file: 2.06924 Thickness value
calculated: 2.44
Example #2 Pial left: -17.137926 -87.548676 30.134594 Thickness left: 001 -17.27066 -85.21771
29.78851 2.13066
Thickness value from file: 2.13066 Thickness value
calculated: 2.3603
If the thickness values from l/rh.thickness are correct and
not the pure 3d euclidean distances, what factor makes the
difference
between them?
Cheers,
Denny
-----Ursprüngliche Nachricht----- Von: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 30. Dezember 2009 22:15 An: Milakara, Denny Cc: FreeSurfer Forum Betreff: Re: [Freesurfer] Pial surface of both hemispheres as specific ASCII output
Hi Denny,
the number of vertices for the pial surface should be
identical to
the # in the white surface. The thickness is a property of both surfaces, and can be associated with either.
cheers Bruce On Thu, 31 Dec 2009, Denny Milakara wrote:
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
>>>>>>>> >>>>>>>> >>>>>>>> >>>> >> >>
a ?h.thickness file has negative thickness values? That should never occur. You can drop the subject on our website and we'll figure out what's going on if you want
cheers, Bruce On Wed, 27 Jan 2010, Milakara, Denny wrote:
I see the point.
In the file with 183284 vertices there are 14 negative thickness values ranging between -0.0002 and -0.2413. How do you explain the negative thickness values, or in another words what should I do with them?
Cheers, Denny
-----Ursprüngliche Nachricht----- Von: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 27. Januar 2010 02:06 An: Milakara, Denny Cc: FreeSurfer Forum Betreff: Re: [Freesurfer] Pial surface of both hemispheres as specific ASCII output
Hi Denny,
in general the lines won't be perpindicular to both tangent planes. Using the surface normal to compute thickness fails dramatically in some cases (which is why we don't use it). Consider a flat bottomed U for the pial surface with a larger flat bottomed U for the white surface. Near the edges of the larger (white) U the surface normal is parallel to the pial surface and hence never intersects it.
cheers, Bruce
On Wed, 27 Jan 2010, Milakara, Denny wrote:
How different is your method from using lines perpendicular
to tangent planes touching both pial and white surface vertices?
Cheers, Denny
-----Ursprüngliche Nachricht----- Von: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 27. Januar 2010 01:36 An: Milakara, Denny Cc: FreeSurfer Forum Betreff: Re: [Freesurfer] Pial surface of both hemispheres as specific ASCII output
Hi Denny,
the thickness we use is the shortest distance to the white surface from each point on the pial surface averaged with the shortest distance to the pial surface from each point on the white surface.
cheers Bruce On Wed, 27 Jan 2010, Milakara, Denny wrote:
Hi Doug,
I'm a bit confused because the thickness values from the
thickness file is not identical to the euclidean distances I calculated myself. Calculated value is always a bit greater.
Example #1 Pial left: -16.679081 -87.523453 30.427801 Thickness left: 000 -16.95796 -85.12147
30.10204 2.06924
Thickness value from file: 2.06924 Thickness value
calculated: 2.44
Example #2 Pial left: -17.137926 -87.548676 30.134594 Thickness left: 001 -17.27066 -85.21771
29.78851 2.13066
Thickness value from file: 2.13066 Thickness value
calculated: 2.3603
If the thickness values from l/rh.thickness are correct and
not the pure 3d euclidean distances, what factor makes the
difference
between them?
Cheers,
Denny
-----Ursprüngliche Nachricht----- Von: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 30. Dezember 2009 22:15 An: Milakara, Denny Cc: FreeSurfer Forum Betreff: Re: [Freesurfer] Pial surface of both hemispheres as specific ASCII output
Hi Denny,
the number of vertices for the pial surface should be
identical to
the # in the white surface. The thickness is a property of both surfaces, and can be associated with either.
cheers Bruce On Thu, 31 Dec 2009, Denny Milakara wrote:
> 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
>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>> >>> >>> > > >
Should I send thickness only or with pial files? I'll also find all negatives and send them in binary mat file, but it can be of other type. How can I send these files?
Cheers, denny
-----Ursprüngliche Nachricht----- Von: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 27. Januar 2010 02:28 An: Milakara, Denny Cc: FreeSurfer Forum Betreff: Re: [Freesurfer] Pial surface of both hemispheres as specific ASCII output
a ?h.thickness file has negative thickness values? That should never occur. You can drop the subject on our website and we'll figure out what's going on if you want
cheers, Bruce On Wed, 27 Jan 2010, Milakara, Denny wrote:
I see the point.
In the file with 183284 vertices there are 14 negative
thickness values ranging between -0.0002 and -0.2413.
How do you explain the negative thickness values, or in
another words what should I do with them?
Cheers, Denny
-----Ursprüngliche Nachricht----- Von: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 27. Januar 2010 02:06 An: Milakara, Denny Cc: FreeSurfer Forum Betreff: Re: [Freesurfer] Pial surface of both hemispheres as specific ASCII output
Hi Denny,
in general the lines won't be perpindicular to both
tangent planes.
Using the surface normal to compute thickness fails
dramatically in
some cases (which is why we don't use it). Consider a flat bottomed U for the pial surface with a larger flat bottomed U for the white surface. Near the edges of the larger (white) U the surface normal is parallel to the pial surface and hence never intersects it.
cheers, Bruce
On Wed, 27 Jan 2010, Milakara, Denny wrote:
How different is your method from using lines perpendicular
to tangent planes touching both pial and white surface vertices?
Cheers, Denny
-----Ursprüngliche Nachricht----- Von: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 27. Januar 2010 01:36 An: Milakara, Denny Cc: FreeSurfer Forum Betreff: Re: [Freesurfer] Pial surface of both hemispheres as specific ASCII output
Hi Denny,
the thickness we use is the shortest distance to the
white surface
from each point on the pial surface averaged with the shortest distance to the pial surface from each point on the
white surface.
cheers Bruce On Wed, 27 Jan 2010, Milakara, Denny wrote:
Hi Doug,
I'm a bit confused because the thickness values from the
thickness file is not identical to the euclidean distances I calculated myself. Calculated value is always a bit greater.
Example #1 Pial left: -16.679081 -87.523453 30.427801 Thickness left: 000 -16.95796 -85.12147
30.10204 2.06924
Thickness value from file: 2.06924 Thickness value
calculated: 2.44
Example #2 Pial left: -17.137926 -87.548676 30.134594 Thickness left: 001 -17.27066 -85.21771
29.78851 2.13066
Thickness value from file: 2.13066 Thickness value
calculated: 2.3603
If the thickness values from l/rh.thickness are correct and
not the pure 3d euclidean distances, what factor makes the
difference
between them?
Cheers,
Denny
> -----Ursprüngliche Nachricht----- > Von: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Gesendet: Mittwoch, 30. Dezember 2009 22:15 > An: Milakara, Denny > Cc: FreeSurfer Forum > Betreff: Re: [Freesurfer] Pial surface of both hemispheres as > specific ASCII output > > Hi Denny, > > the number of vertices for the pial surface should be
identical to
> the # in the white surface. The thickness is a
property of both
> surfaces, and can be associated with either. > > cheers > Bruce > On Thu, 31 Dec 2009, Denny Milakara wrote: > >> 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
>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>> >>>> >>>> >> >> >> >
you can check our website, and the best thing to do is to tar and gzip the whole subject and send it to us
On Wed, 27 Jan 2010, Milakara, Denny wrote:
Should I send thickness only or with pial files? I'll also find all negatives and send them in binary mat file, but it can be of other type. How can I send these files?
Cheers, denny
-----Ursprüngliche Nachricht----- Von: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 27. Januar 2010 02:28 An: Milakara, Denny Cc: FreeSurfer Forum Betreff: Re: [Freesurfer] Pial surface of both hemispheres as specific ASCII output
a ?h.thickness file has negative thickness values? That should never occur. You can drop the subject on our website and we'll figure out what's going on if you want
cheers, Bruce On Wed, 27 Jan 2010, Milakara, Denny wrote:
I see the point.
In the file with 183284 vertices there are 14 negative
thickness values ranging between -0.0002 and -0.2413.
How do you explain the negative thickness values, or in
another words what should I do with them?
Cheers, Denny
-----Ursprüngliche Nachricht----- Von: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 27. Januar 2010 02:06 An: Milakara, Denny Cc: FreeSurfer Forum Betreff: Re: [Freesurfer] Pial surface of both hemispheres as specific ASCII output
Hi Denny,
in general the lines won't be perpindicular to both
tangent planes.
Using the surface normal to compute thickness fails
dramatically in
some cases (which is why we don't use it). Consider a flat bottomed U for the pial surface with a larger flat bottomed U for the white surface. Near the edges of the larger (white) U the surface normal is parallel to the pial surface and hence never intersects it.
cheers, Bruce
On Wed, 27 Jan 2010, Milakara, Denny wrote:
How different is your method from using lines perpendicular
to tangent planes touching both pial and white surface vertices?
Cheers, Denny
-----Ursprüngliche Nachricht----- Von: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 27. Januar 2010 01:36 An: Milakara, Denny Cc: FreeSurfer Forum Betreff: Re: [Freesurfer] Pial surface of both hemispheres as specific ASCII output
Hi Denny,
the thickness we use is the shortest distance to the
white surface
from each point on the pial surface averaged with the shortest distance to the pial surface from each point on the
white surface.
cheers Bruce On Wed, 27 Jan 2010, Milakara, Denny wrote:
> Hi Doug, > > > I'm a bit confused because the thickness values from the thickness file is not identical to the euclidean distances I calculated myself. Calculated value is always a bit greater. > > > Example #1 > Pial left: -16.679081 -87.523453 30.427801 > Thickness left: 000 -16.95796 -85.12147 30.10204 2.06924 > Thickness value from file: 2.06924 Thickness value
calculated: 2.44
> > > Example #2 > Pial left: -17.137926 -87.548676 30.134594 > Thickness left: 001 -17.27066 -85.21771 29.78851 2.13066 > Thickness value from file: 2.13066 Thickness value calculated: 2.3603 > > If the thickness values from l/rh.thickness are correct and not the pure 3d euclidean distances, what factor makes the
difference
between them? > > > Cheers, > > Denny > > > >> -----Ursprüngliche Nachricht----- >> Von: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] >> Gesendet: Mittwoch, 30. Dezember 2009 22:15 >> An: Milakara, Denny >> Cc: FreeSurfer Forum >> Betreff: Re: [Freesurfer] Pial surface of both hemispheres as >> specific ASCII output >> >> Hi Denny, >> >> the number of vertices for the pial surface should be
identical to
>> the # in the white surface. The thickness is a
property of both
>> surfaces, and can be associated with either. >> >> cheers >> Bruce >> On Thu, 31 Dec 2009, Denny Milakara wrote: >> >>> 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 >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>> >>>>> >>>>> >>> >>> >>> >> > > >
Hi,
I analyze brains with subarachnoidal hemorrhage and often they look messy. Not only because of the blood on the pial surface, but also changed WM/GM CNR due to ischemia or edema, and deformations after the surgical decompression. Is there a workaround to include the blood layer/clot into to segmentation output, something like pre-segmentation labeling?
Cheers, Denny
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Denny Milakara -
Milakara, Denny