[Freesurfer] get non-cortex vertices

Hi freesurfers, I am doing a connectivity analysis on cortical areas. I load the 2d fmri surface file in fsaverage5 space into matlab and I get 20484 vertices for both hemispheres. Some of which are zero because I previously specified to get only the cortex vertices. However, the number of non-cor

Re: [Freesurfer] get non-cortex vertices

27;s brain is > different, and you can't get a subject-specific mask from fsaverage5. Can > you load all your data into matlab and then compute a mask based on > non-zero voxels? > > On 9/28/16 1:57 PM, Dorothy Sincasto wrote: > > Hi freesurfers, > > I am doing a connectivity a

[Freesurfer] Mris_decimate for MAC

Hi, I can't find in my freesurfer version the mri_decimate, and I tried to download it from the links in the mailing list archive but they are down. >From where could I download it? Thanks Dorothy ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard

Re: [Freesurfer] Mris_decimate for MAC

n 11/18/2016 07:26 PM, Dorothy Sincasto wrote: > > Hi, > > > > I can't find in my freesurfer version the mri_decimate, and I tried to > > download it from the links in the mailing list archive but they are down. > > > >

Re: [Freesurfer] Mris_decimate for MAC

nload from here: > >https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall6.0-beta > > Hope this helps. > > On 11/21/2016 09:21 AM, Dorothy Sincasto wrote: > > Hi Zake > > > > Actually, it was you in one of the emails who linked a version for MAC: > > h

[Freesurfer] MEG time series to surface overlay

Hi, I have MEG time series for every vertex in a decimated surface (~6000 vertices). I want to create a file (i think is called overlay) in which the timeseries are saved, like an fMRI mgz overlay. How can I do that with matlab? I have tried read_surf for reading the midthickness surface file, an

Re: [Freesurfer] MEG time series to surface overlay

fwrite3(fid, v(i)) ; % vertex number (0-based) Thanks Dorothy On Tue, Mar 14, 2017 at 7:28 PM, Bruce Fischl wrote: > Can you send us the full command you ran and the full screen output? > > Thanks > Bruce > > > On Mar 14, 2017, at 9:33 PM, Dorothy Sincasto >

Re: [Freesurfer] MEG time series to surface overlay

; > ntimepoints and use MRIwrite or save_mgh > > > > On Wed, 15 Mar 2017, Dorothy Sincasto wrote: > > > >> Hi Bruce, > >> first I do: > >> > >> [vertex_coords, faces, magic] = > >> read_surf('rh.13475.midthickness.decimated.05.s

[Freesurfer] Surface down sample by taking cortical vertices only

Hi I want to do an MEG analysis and first I want to downsample the surface to around 100 vertices per hemisphere. I tried the command mris_downsample, but when i plot the surface I see that the vertices go deep into the white matter. Is there an option to extract for example 100 equidistant vert

Re: [Freesurfer] Surface down sample by taking cortical vertices only

On Mon, Apr 10, 2017 at 2:42 PM, Dorothy Sincasto > wrote: > > Hi > > > > I want to do an MEG analysis and first I want to downsample the surface > to > > around 100 vertices per hemisphere. I tried the command mris_downsample, > > but when i plot the surface I s

[Freesurfer] decimate overlay

Hi freesurfers, I have an overlay with 4k vertices and I want to decimate it to 1k. This overlay is actually an atlas with a label value for each vertex. My surfaces will have 1k vertices and I need the overlay to 1k so I know which areas each vertex belong to. I tried to decimate the atlas.mgh b

Re: [Freesurfer] decimate overlay

find the nearest vertices in the 4k. Thanks Dorothy On Mon, May 15, 2017 at 6:49 PM, Douglas Greve wrote: > I don't understand what you are trying to do. Can you elaborate? Sending > command lines is always helpful > > On 5/15/17 6:50 PM, Dorothy Sincasto wrote: > > Hi fre

Re: [Freesurfer] decimate overlay

--streg surf4k > surf1k > > On 5/16/17 12:41 PM, Dorothy Sincasto wrote: > > Hi Douglas, > > I am using the cortical surface for MEG time series reconstruction. I need > to know which vertices belong to a specific area, i.e. vertices that > belong to the PCC, AG... I got

[Freesurfer] Freesurfer surface to Fieldtrip SPM

Hi I've been struggling to convert a freesurfer surface into an MNI space coordinate. I tried to follow some tutorials and to play around with transformation matrices but nothing works. I have an MNI surface from freesurfer (the cvs_avg35_inMNI152) and I need to align it to the 3d MNI 152. When l

[Freesurfer] Gray matter normalized intensity

External Email - Use Caution Dear Freesurfers Usually, the mean normalized intensity in aseg.stats is not considered important. However, by mistake, I put it in my analysis and found out that the mean intensity of the thalamus explains a lot the variance of my data. What could be

Re: [Freesurfer] Gray matter normalized intensity

take out the contribution of cortical gray matter and just leave the level of thalamic myelinization. Regards Dorothy On Thu, Mar 21, 2019 at 6:48 PM Glasser, Matthew wrote: > External Email - Use Caution > > What is the other variable? > > Matt. > > From: on behalf