Re: [Freesurfer] mris_wm_volume

Hi Nick, Thanks for the tool. I am getting output of 0 with >mris_wm_volume con_2304 lh 0 This follows the usage as I see it. Am I using this wrong? Cheers, -Morgan Nick Schmansky wrote: Morgan, I've posted mris_wm_volume for the various platforms at this location: ftp://surfer.nmr.mgh.

[Freesurfer] Create thickness map

Hello, Is it possible to create a "fake" thickness map in order to perform some tests? Thanks, Ines ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] How to analysis animal data

I know someone here have successfully apply freesurfer on monkey. Do you mind to describe how you can do that? Freesurfer is closely related to human atlas. If you need to apply it on animal, like monkey, do you need to contruct a monkey atlas? Anything besides atlas that need to take care? than

Re: [Freesurfer] mris_wm_volume

that looks like the correct usage. Can you send the entire screen output? On Fri, 20 Jul 2007, Morgan Hough wrote: Hi Nick, Thanks for the tool. I am getting output of 0 with mris_wm_volume con_2304 lh 0 This follows the usage as I see it. Am I using this wrong? Cheers, -Morgan Nick Sc

Re: [Freesurfer] Create thickness map

sure. Do it in matlab and use save_mgh to save it as a "volume" with dimensions nverticesx1x1. You can get the # of vertices using mris_euler_number or mris_info. cheers, Bruce On Fri, 20 Jul 2007, Inês Souta wrote: Hello, Is it possible to create a "fake" thickness map in order to perfo

Re: [Freesurfer] How to analysis animal data

Hi Ian, yes, it has been used on lots of monkey brains. I would contact Wim Vanduffel or Roger Tootell (both ccd). cheers, Bruce On Fri, 20 Jul 2007, lan lin wrote: I know someone here have successfully apply freesurfer on monkey. Do you mind to describe how you can do that? Freesurfer i

Re: [Freesurfer] Intersecting surfaces (thickness = 0mm)

Hi Inge, that looks like posterior hippocampus. We constrain the pial and white surfaces to not move in non-cortical regions so that they don't contribute to the volume/surface area of the ribbon. There's a label named ?h.cortex.label that is automatically created that gives the region of the

[Freesurfer] statistical designs

Hello, group I want to learn more about designs of the general linear models for different statistical tests, such as paired T, ANOVA, and correlation tests. Could anybody suggest some examples of the designs for each model? I am facing a few problems of correlation analysis. If I want to do the

Re: [Freesurfer] statistical designs

Check out http://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/freesurfer.groupanalysis.pdf for some answers. For paired-t, you can specify --paired-diff to mris_preproc Wang, Xin wrote: Hello, group I want to learn more about designs of the general linear models for different statistical

Re: [Freesurfer] Create thickness map

if you want to fill it with white-gaussian noise, you can also use mri_surf2surf, something like mri_surf2surf --s yoursubject --hemi lh --sval lh.thickness --tval lh.thickness.synth -tfmt curv --synth if you want more elaborate distributions, you can use mri_volsynth then mri_surf2surf (don

[Freesurfer] Skull Stripping Corrections

Hello- I've been working through the Skull Stripping checking/corrections tutorial and have a question. So far, I have found no problems akin to the tutorial, where skull is left behind or brain parts are missing. However, I do see remnants of eyeballs/eye sockets, arteries, and dura/pia/meni

RE: [Freesurfer] Skull Stripping Corrections

Hi Jim, You really only need to be concerned about these issues you've shown if they begin to affect your surfaces - that is, if the pial or white surface includes these regions that it shouldn't. If your surfaces are fine, you can leave this alone! Jenni -Original Message- From: [EMAIL

RE: [Freesurfer] statistical designs

Thank you, Doug. Do you have more examples of different designs? Could anyone answer the rest of my questions? Thank you again, Xin From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Fri 7/20/2007 2:45 PM To: Wang, Xin Cc: freesurfer Subject: Re: [Freesurf

Re: [Freesurfer] statistical designs

If you want to do a within group analysis, just declare one class. Correlation tests boil down to testing a continuous variable in a glm. I don't have anything which will compute a correlation coefficient, though it is a good idea. As for the # of subjects, that's a power question. doug W

[Freesurfer] Connecting Vertex Points in FreeSurfer

Hi Everybody,I am bringing in talairach points into freesurfer by converting them into vertexes. I need to connect all of them to create a colored label showing the area bounded by these vertex points. However, I can't seem to find a way to connect these vertexes in a specified manner. I would g

Re: [Freesurfer] Connecting Vertex Points in FreeSurfer

Hi Troy, can you explain what your goal is? In general a talairach point won't be near the surface, and the intersection of a set of talairach points with the surface (e.g. a ball in tal coords) will have an arbitrary topology on the folded surface. Bruce On Fri, 20 Jul 2007, Troy Mcan wrot