Re: [Freesurfer] What is MNI coordinates

Hi BOBO, There are 2 popular atlases the Talairach (which was developed from a single female brain) and the MNI (which has been developed on an average of several adult brains). MNI coordinates is basically co-ordinates of the MNI space and extremely popular and well-used in the neuroimaging mo

[Freesurfer] What is MNI coordinates

Dear FreeSurfer experts Recently,I am learning FreeSurfer and I see a word 'MNI coordinates'.What is MNI coordinates?Can you give me some essays about it? thanks very much BOBO ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail

[Freesurfer] How can I get the mean thickness of the significant cluster

Dear Freesurfer experts, I have done the whole brain analysis and get some significant clusters. How can I get the mean thickness of these clusters of every subject? Thank you very much. Mingxia Zhang ___ Freesurfer mailing list Freesurfer@nmr.mgh.harv

Re: [Freesurfer] Gcut contrast change

Yes, thanks BruceI'd checked the intensity values, and they were exactly the same as before the skull strippingRegards,GabrielEl 09/04/12, Bruce Fischl escribió:Hi Gabrielthe contrast probably isn't changed, just the display. Tkmedit tries to compute good window level settings based on the image

Re: [Freesurfer] Freeview bus error

According to freesurfer release notes http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes, Freeview in version 5.0 does not work on Snow Leopard. Version 5.1 has fixed it. Ruopeng On 04/10/2012 04:36 PM, Jeni Chen wrote: Hi, I was recently at the FreeSurfer workshop in Boston and learned a

[Freesurfer] Freeview bus error

Hi, I was recently at the FreeSurfer workshop in Boston and learned about the "Freeview" tool in Freesurfer. However, when I tried to run it from my own laptop (Mac book pro), it crashes and gives the error message: "Bus error". I didn't get a chance to have this problem solved while I was the

Re: [Freesurfer] Empty Segmentations

Hi All, I think this problem was just due to two different versions of parcellation/segmentation nomenclature. Allie On Tue, Apr 10, 2012 at 1:34 PM, Allie Rosen wrote: > Hello Again, > > If this helps, all the subjects who have empty segmentations in the first > series of measures below, ar

Re: [Freesurfer] Empty Segmentations

Hello Again, If this helps, all the subjects who have empty segmentations in the first series of measures below, are not empty in the second series, and vice versa. I'm wondering if there are multiple files from which this information should be pulled, rather than just aseg. stats Thank you, Alli

Re: [Freesurfer] question abt fsaverage_sym

On 04/10/2012 10:04 AM, Ritobrato Datta wrote: > Hi Doug, > > I am following up on the post below > > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-February/022613.html > > Question 1) How is the new fsaverage_sym different from the old one ? There was a small bug in the constructio

Re: [Freesurfer] Identifying meridia in retinotopic maps

On 04/10/2012 09:40 AM, Greg Burgess wrote: > HI freesurfers, > > I have a few questions that were asked previously, but I don't seem to be > able to find (or possibly understand) the answers. > 1) I'm displaying polar and eccentricity maps using the rtview script. > However, no color wheel app

Re: [Freesurfer] How to let fsfast process the data not named f.nii.gz?

Can you change the name or create a symlink? It will be much easier ... On 04/10/2012 12:42 AM, Zhen Zonglei wrote: > > My raw BOLD data is named func.nii.gz in each run directory. It > preprocess-sess reported the ERROR: could not determine format for > S0001/obj/004/f, even I provide the –ifun

[Freesurfer] recon-all processing stages

Hi I'm not sure but does the Talairach stage precede the nu-correct stage in version v5.1.0? If so, is there an option to switch these two stages? Cheers, Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/ma

[Freesurfer] Empty Segmentations

Hi Freesurfers, I am attempting to get total GM and WM volumes for two populations. I ran asegstats2table. For the following segmentations, 6/8 control measures are empty: lhCortexVol rhCortexVol CortexVol lhCorticalWhiteMatterVol rhCorticalWhiteMatterVol SubCortGrayVol TotalGrayVol For the fo

Re: [Freesurfer] Clarification on centos version/updates/patches

Wil, Hi, the contents of that 'misc' directory is just a filedrop of sorts to supply fixes to individuals who need particular updates. We dont supply formal patches, as it gets too unwieldy to track versions. Rather bug fixes are documented (mostly!) on the ReleaseNotes page with links to fixes.

[Freesurfer] Identifying meridia in retinotopic maps

HI freesurfers, I have a few questions that were asked previously, but I don't seem to be able to find (or possibly understand) the answers. 1) I'm displaying polar and eccentricity maps using the rtview script. However, no color wheel appears, and I do not seem to be able to find an option to