Re: [Freesurfer] Talairach coordinates
Feng-Xian, The coordinates are surface coordinates. qdec does not display the Tal coords, but I think this will be added in a future release. You can get the Tal coords using tksurfer. The surface displayed in qdec is the 'fsaverage' surface, so that can be loaded in tksurfer. First, in qdec, make note of the vertex number that you are displaying for your plot. Then load fsaverage in tksurfer: tksurfer fsaverage lh inflated (or 'rh' if right hemi). then, select Tools->Select Vertex and enter the vertex number. you should see the point highlighted in blue on the surface. the tal coords will be displayed in the tools window. you can get MNI tal coords by selecting View->Information- >Vertex MNI Talairach Nick On Sun, 2008-06-29 at 22:10 +0800, Feng-Xian Yan wrote: > > Hi, > I have some problems about surface coordinates. > After running the qdec and analyzed my data(cortical thickness), I > display a plot of the data for a particular vertex by left-clicking on > a point while holding down the Ctrl key. It shows a plot and its plot > window shows this vertex's surface coordinates. > 1) Does the surface coordinates differ from Talairach coordinates? > 2) If yes, can I translate the surface coordinates to Talairach > coordinates? > And how do I do? Does Freesurfer have some methods to do that? > > Thank you in advance. > Feng-Xian > > ___ > 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
Re: [Freesurfer] Talairach coordinates
Nick, When you cite this cordinates in a paper, what is the name you use? Best Regards, PPJ 2008/7/8 Nick Schmansky <[EMAIL PROTECTED]>: > Feng-Xian, > > The coordinates are surface coordinates. qdec does not display the Tal > coords, but I think this will be added in a future release. > > You can get the Tal coords using tksurfer. The surface displayed in > qdec is the 'fsaverage' surface, so that can be loaded in tksurfer. > First, in qdec, make note of the vertex number that you are displaying > for your plot. Then load fsaverage in tksurfer: > > tksurfer fsaverage lh inflated > > (or 'rh' if right hemi). > > then, select Tools->Select Vertex > and enter the vertex number. you should see the point highlighted in > blue on the surface. the tal coords will be displayed in the tools > window. you can get MNI tal coords by selecting View->Information- > >Vertex MNI Talairach > > Nick > > > On Sun, 2008-06-29 at 22:10 +0800, Feng-Xian Yan wrote: > > > > Hi, > > I have some problems about surface coordinates. > > After running the qdec and analyzed my data(cortical thickness), I > > display a plot of the data for a particular vertex by left-clicking on > > a point while holding down the Ctrl key. It shows a plot and its plot > > window shows this vertex's surface coordinates. > > 1) Does the surface coordinates differ from Talairach coordinates? > > 2) If yes, can I translate the surface coordinates to Talairach > > coordinates? > > And how do I do? Does Freesurfer have some methods to do that? > > > > Thank you in advance. > > Feng-Xian > > > > ___ > > 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 > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Talairach coordinates
the surface coords aren't useful to cite as they are not consistent cross-subject. We could display spherical and tal I guess. That would be the most useful On Tue, 8 Jul 2008, Pedro Paulo de Magalhães Oliveira Junior wrote: Nick, When you cite this cordinates in a paper, what is the name you use? Best Regards, PPJ 2008/7/8 Nick Schmansky <[EMAIL PROTECTED]>: Feng-Xian, The coordinates are surface coordinates. qdec does not display the Tal coords, but I think this will be added in a future release. You can get the Tal coords using tksurfer. The surface displayed in qdec is the 'fsaverage' surface, so that can be loaded in tksurfer. First, in qdec, make note of the vertex number that you are displaying for your plot. Then load fsaverage in tksurfer: tksurfer fsaverage lh inflated (or 'rh' if right hemi). then, select Tools->Select Vertex and enter the vertex number. you should see the point highlighted in blue on the surface. the tal coords will be displayed in the tools window. you can get MNI tal coords by selecting View->Information- Vertex MNI Talairach Nick On Sun, 2008-06-29 at 22:10 +0800, Feng-Xian Yan wrote: Hi, I have some problems about surface coordinates. After running the qdec and analyzed my data(cortical thickness), I display a plot of the data for a particular vertex by left-clicking on a point while holding down the Ctrl key. It shows a plot and its plot window shows this vertex's surface coordinates. 1) Does the surface coordinates differ from Talairach coordinates? 2) If yes, can I translate the surface coordinates to Talairach coordinates? And how do I do? Does Freesurfer have some methods to do that? Thank you in advance. Feng-Xian ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] deflate compression support
Jan, It appears that the libtiff used to build mris_make_template did not have deflate (zip) support. An updated binary can be downloaded from here: wget ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable/macintel/mris_make_template the wget command is one line. run this command in the /Applications/freesurfer/bin directory, then type: chmod a+x /Applications/freesurfer/bin/mris_make_template Nick On Tue, 2008-07-01 at 11:27 -0400, Jan Kalkus wrote: > Hi everyone, > > I'm trying to make a monkey template using mris_make_template. So > far, every time I run the mris_make_template, I get this error: > > [jkalkus:~] work% /Volumes/Data/monkey_surface_data/mris_make > creating new parameterization... > > processing subject bu_edited (1 of 1) > reading spherical surface /Volumes/Data/monkey_surface_data//bu_edited/ > surf/rh.sphere... > curvature mean = 0.000, std = 1.000 > computing parameterization for surface /Volumes/Data/ > monkey_surface_data//bu_edited/surf/rh.inflated.H... > curvature mean = 0.000, std = 0.592 > computing parameterization for surface /Volumes/Data/ > monkey_surface_data//bu_edited/surf/rh.sulc... > curvature mean = -0.100, std = 1.787 > computing parameterization for surface /Volumes/Data/ > monkey_surface_data//bu_edited/surf/rh.smoothwm... > writing updated template with 1 subjects to monk_temp0.tif... > monk_temp0.tif: Deflate compression support is not configured. > TiffWrite: TIFFWriteScanline returned error > > I am working on an intel MacBook with OS X 10.5.4 and I'm running > freesurfer-Darwin-leopard-i686-stable-pub-v4.0.5. Has anyone else > encountered this problem? Does anyone have any suggestions? Thanks > > - Jan Kalkus > ___ > 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
