[Freesurfer] Merging Brain Hemispheres

Hello, As we know, Freesurfer generates separate surface models and associated labels for each brain hemisphere, is there any way to merge two hemisphere and come up with a single cortex surface? My best, Saeed ___ Freesurfer mailing list Freesurfer@nm

[Freesurfer] (no subject)

Hello, As we know, Freesurfer generates separate surface models and associated labels for each brain hemisphere, is there any way to merge two hemisphere and come up with a single cortex surface? My best, Saeed ___ Freesurfer mailing list Freesurfer@nmr

[Freesurfer] Volumetric measurments and difference between results from "recon_all" and "mri_segstats"

Hello Folks, I used the recon-all -i -all -segmentation for the structural image. FreeSurfer makes several folder and one of them is "stats". In this folder, there is aseg.stats that includes volume of different brain regions. Also, I found "mri_segstats" command line that gives us the volume of

[Freesurfer] Brain on a Single Sphere

Hello Experts, Is there any command that can map both hemispheres of the brain into one single sphere? It will be equal to combining two inflated hemispheres into one spherical brain surface that has its own scalar overlays. Best, Saeed ___ Freesurfer m

Re: [Freesurfer] Label or Overlay of Surface files

SOLVED. On Fri, Aug 14, 2015 at 4:08 PM, Saeed Mahdizadeh Bakhshmand < saeedbakhshm...@gmail.com> wrote: > Hello, > > I am trying to load surface overlays in 3D Slicer on top of surface meshes > (e.g. lh.Inflated), > but surface overlays somehow don't load properly int

Re: [Freesurfer] Label or Overlay of Surface files

Hello, I am trying to load surface overlays in 3D Slicer on top of surface meshes (e.g. lh.Inflated), but surface overlays somehow don't load properly into 3D slicer, I am trying right surface files (lh.sulc , lh.curve e.g.)? On Fri, Aug 7, 2015 at 10:14 AM, Saeed Mahdizadeh Bakhs

Re: [Freesurfer] Fwd: Inflated and Spherical Morphing --- Step by step surfaces

chl wrote: > I guess only by looking at the code. We have tried to flesh out most of > the documentation but have limited resources and person-power (and > funding!) to do so. > > sorry > Bruce > > > > On Fri, 7 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: > >

Re: [Freesurfer] Fwd: Inflated and Spherical Morphing --- Step by step surfaces

gt; we normally project onto the sphere, but if you want to generate a movie > to show the idea you can give mris_sphere the flag -i, which will cause it > to inflate to the sphere before unfolding. > > cheers > Bruce > > > On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrot

Re: [Freesurfer] Label or Overlay of Surface files

surface -snap -curv > > Best, > Lee > > > On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: > > I used it as this:tksurfer subject hemisphere surface -snap >> -overlay >> And it adds a gray scale version of sulcus map to the plain gray, How can >>

Re: [Freesurfer] Fwd: Inflated and Spherical Morphing --- Step by step surfaces

d and inflated to a sphere. On Aug 6, 2015 7:45 PM, "Bruce Fischl" wrote: > yes, because it is unfolding on the sphere to recover metric properties. > -w 1 gives you every iteration. You will need to show curvature or you > won't see anything > > On Thu, 6 Aug 2015,

Re: [Freesurfer] Fwd: Inflated and Spherical Morphing --- Step by step surfaces

> of the process every nth iteration > cheers > Bruce > > > On Wed, 5 Aug 2015, > Saeed Mahdizadeh Bakhshmand wrote: > > > Hello, > > > > Since surface deformation from WM to inflated surface is a gradual > process, > > I assume that interim surfaces c

Re: [Freesurfer] Label or Overlay of Surface files

rs > Bruce > > > On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: > > And are they treated as label files (e.g. lh.aparc.annot ) in the label >> directory? And how they can be added to the tksurfer snapshot procedure? >> >> On Thu, Aug 6, 2015 at 4:04 PM, B

Re: [Freesurfer] Label or Overlay of Surface files

t; On Thu, 6 Aug 2015, Saeed Mahdizadeh Bakhshmand wrote: > > Hello, >> Is scalar overlay information embedded into surface file itself? When I >> open >> them in freeview they are loaded with color overlays (sulcus/gyrus), but >> when I load same models into 3D slic

[Freesurfer] Label or Overlay of Surface files

Hello, Is scalar overlay information embedded into surface file itself? When I open them in freeview they are loaded with color overlays (sulcus/gyrus), but when I load same models into 3D slicer or take a snapshot in tksurfer, they are plain gray. Thanks, Saeed __

Re: [Freesurfer] Fwd: Inflated and Spherical Morphing --- Step by step surfaces

ot;? On Wed, Aug 5, 2015 at 3:08 PM, Bruce Fischl wrote: > you can use convert to take the multiple tiff files that are written and > output a dynamic gifti > > On Wed, 5 Aug 2015, Saeed > Mahdizadeh Bakhshmand wrote: > > > Thanks Bruce, and Is there an easy way to make a

Re: [Freesurfer] Fwd: Inflated and Spherical Morphing --- Step by step surfaces

gt; > On Wed, 5 Aug 2015, > Saeed Mahdizadeh Bakhshmand wrote: > > > Hello, > > > > Since surface deformation from WM to inflated surface is a gradual > process, > > I assume that interim surfaces can also be saved and visualized, as I > have > > s

[Freesurfer] Fwd: Inflated and Spherical Morphing --- Step by step surfaces

Hello, Since surface deformation from WM to inflated surface is a gradual process, I assume that interim surfaces can also be saved and visualized, as I have seen in the ppt of "Analyzing the Individual Subject " tutorial session (sli