[Freesurfer] ascii information file for a label
Hi, Tksurfer provides a nice tool to display information such as vertex index, spherical coordinates (rho, theta), values of overlaid functionals as a function of the mouse/cursor position. I wonder if there is a way to save all information above (index, spherical coordinates, overlaid functionals values) into an ascii text file for all vertexes located within a certain label (patch)? Something like mris_convert -p *h.patch.flat *h.patch.flat.asc that in addition to vertex number, provides spherical coordinates, AND values of functional overlay(s) for a patch, or better for a label. Thank you, Serge ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ascii information file for a label
I wonder if there is a way to save all information above (index, spherical coordinates, overlaid functionals values) into an ascii text file for all vertexes located within a certain label (patch)? The only thing close to this is the Save Summary function for time courses. But it's not going to save all the information you want, so, sorry, but no. -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ascii information file for a label
if you save a label with a statistical overlay, the stat field in the label (the last field in each row) should have the statistic at that point. Isn't that right Kevin? Bruce On Thu, 6 Jan 2005, Kevin Teich wrote: I wonder if there is a way to save all information above (index, spherical coordinates, overlaid functionals values) into an ascii text file for all vertexes located within a certain label (patch)? The only thing close to this is the Save Summary function for time courses. But it's not going to save all the information you want, so, sorry, but no. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ascii information file for a label
That's true; you'll get an index, original RAS coordinates, and the overlay value for each vertex in the label. On Thu, 6 Jan 2005, Bruce Fischl wrote: if you save a label with a statistical overlay, the stat field in the label (the last field in each row) should have the statistic at that point. Isn't that right Kevin? Bruce On Thu, 6 Jan 2005, Kevin Teich wrote: I wonder if there is a way to save all information above (index, spherical coordinates, overlaid functionals values) into an ascii text file for all vertexes located within a certain label (patch)? The only thing close to this is the Save Summary function for time courses. But it's not going to save all the information you want, so, sorry, but no. -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ascii information file for a label
Hi Serge, convert the ?h.sphere.reg file to ascii format, and lookup the verices in it. That will give you (x,y,z) that you can convert to (rho,theta) On Thu, 6 Jan 2005, Sergey A Solovyev wrote: Many thanks, it works great. The remaining problem is to convert vertex indexes/RAS coordinates into spherical coordinates (rho,theta), ascii text file, or print all spherical coordinates for a patch/label. --Serge Kevin Teich wrote: That's true; you'll get an index, original RAS coordinates, and the overlay value for each vertex in the label. On Thu, 6 Jan 2005, Bruce Fischl wrote: if you save a label with a statistical overlay, the stat field in the label (the last field in each row) should have the statistic at that point. Isn't that right Kevin? Bruce On Thu, 6 Jan 2005, Kevin Teich wrote: I wonder if there is a way to save all information above (index, spherical coordinates, overlaid functionals values) into an ascii text file for all vertexes located within a certain label (patch)? The only thing close to this is the Save Summary function for time courses. But it's not going to save all the information you want, so, sorry, but no. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] normalization failed
Hi, During recon-all -stage1 running, I got the following error. ... MRInormalize: could not find any valid peaks No such file or directory mri_normalize: normalization failed No such file or directory ERROR: mri_normalize exited with non-zero status - Any suggestion would be appreciated. Nam. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] normalization failed
check the talairach transform On Thu, 6 Jan 2005, Joongnam Yang wrote: Hi, During recon-all -stage1 running, I got the following error. ... MRInormalize: could not find any valid peaks No such file or directory mri_normalize: normalization failed No such file or directory ERROR: mri_normalize exited with non-zero status - Any suggestion would be appreciated. Nam. ___ 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
