[Freesurfer] unable to dload freesurfer old versions

Hi, I was trying to download freesurfer realease 4.3 from the archives but unable to do so. Is the website down? freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0-full.tar.gz Be

[Freesurfer] display error

Dear Freesurfer community, I have a display problem that affects especially tkmedit and tksurfer. We run freesurfer ( freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0) on a remote unix server and use Exceed (v. 14.0.0.376) to port the display to a local (windows) computer. At first we got a openG

Re: [Freesurfer] selxavg3 can't find image that exists

Doug - Thanks for the help. A few more questions... 1. Is it worth re-preprocessing with -sliceorder siemens? 2. Does mkanalysis-sess -fwhm 8 -stc siemens -surface fsaverage lh ... not do preprocessing but just uses those specs to build the string for the filename search? Or will it do preproc

[Freesurfer] distance between two points along cortical surface

Hi, How should I have the distance between two points in mm? If I use the ?h.sphere, as all the spherical surfaces are normalized to have 100 radius. so the geodesic distances should not be the real distance in mm? Fariba __ Fariba Sharifian, PhD

[Freesurfer] distance between two points along cortical surface

Hi, How should I have the distance between two points in mm? If I use the ?h.sphere, as all the spherical surfaces are normalized to have 100 radius. so the geodesic distances should not be the real distance in mm? Fariba __ Fariba Sharifian, Ph

Re: [Freesurfer] distance between two points along cortical surface

Hi Fariba, you can scale the sphere to have the same surface area as the ?h.white, then use great circles on it. cheers Bruce On Mon, 11 Apr 2011, Fariba Sharifian wrote: > Hi, > How should I have the distance between two points in mm? > If I use the ?h.sphere, as all the spherical surfaces ar

Re: [Freesurfer] distance between two points along cortical surface

On 4/11/11 09:36 , Fariba Sharifian wrote: > Hi, > How should I have the distance between two points in mm? > If I use the ?h.sphere, as all the spherical surfaces are normalized to > have 100 radius. so the geodesic distances should not be the real > distance in mm? > > Fariba > Another way is t

Re: [Freesurfer] selxavg3 can't find image that exists

Scott Burns wrote: > Doug - > > Thanks for the help. A few more questions... > > 1. Is it worth re-preprocessing with -sliceorder siemens? > depends. If you have an even number of slices, then your slice order is wrong, and you should delete the preprocessed data and start over. If you have

Re: [Freesurfer] Fwd: bbregister bug? with init-spm option--flips left and right

In version 5 there is actually already a flag for this in bbregister. Try running it with --spm-nii. doug Tyler Seibert wrote: > Thanks, Doug and Michael--that did the trick! What is the status of > this issue for newer versions of FreeSurfer (e.g., 5.0)? > > Tyler > > On Tue, Mar 29, 2011 at 8

Re: [Freesurfer] Fwd: bbregister bug? with init-spm option--flips left and right

Great, thanks! On Mon, Apr 11, 2011 at 6:59 AM, Douglas N Greve wrote: > In version 5 there is actually already a flag for this in bbregister. Try > running it with --spm-nii. > doug > > Tyler Seibert wrote: > >> Thanks, Doug and Michael--that did the trick! What is the status of this >> issue fo

Re: [Freesurfer] functional ROI analysis problem

Ok, I ran that and a couple questions. I ran it on 2 different subjects and got the exact same value, is that expected? Do I need to run it for each subject? Also, do I need to do this for event-related designs as well, or just block designs? I tried to run it on another analysis I did, an even

Re: [Freesurfer] functional ROI analysis problem

Yes, it should be the same across all subjects. You only need to do it for designs that use an assumed shape (-gammafit). doug Katie Bettencourt wrote: > Ok, I ran that and a couple questions. I ran it on 2 different > subjects and got the exact same value, is that expected? Do I need to > ru

Re: [Freesurfer] unable to dload freesurfer old versions

I had this problem last Friday with v4.5 centos 64 tar.gz file as well. On Mon, Apr 11, 2011 at 7:04 AM, Nikhil Pratap Singh wrote: > Hi, > > I was trying to download freesurfer realease 4.3 from the archives but > unable to do so. Is the website > down?freesurfer-Linux-centos4_x86_64-stable-

[Freesurfer] Visualizing Subcortical Volume Differences

Hello, I am interested in a way to visualize the differences in the volume in subcortical structures, preferably in 3D. For example, I would like to view the Thalamus of controls. And then I would like to overlay a color-coded map that shows the difference between the volume of the Control Thala

Re: [Freesurfer] unable to dload freesurfer old versions

try the ftp link On Mon, 2011-04-11 at 15:17 -0400, Thomas Ballinger wrote: > I had this problem last Friday with v4.5 centos 64 tar.gz file as > well. > > On Mon, Apr 11, 2011 at 7:04 AM, Nikhil Pratap Singh > wrote: > Hi, > I was trying to download freesurfer realease 4.3 fro

Re: [Freesurfer] unable to dload freesurfer old versions

I had some trouble with ftp but it looks like ftp is working now. Download is in progress. Thanks Nick! Best, Nikhil On 04/11/2011 05:36 PM, Nick Schmansky wrote: > try the ftp link > > > On Mon, 2011-04-11 at 15:17 -0400, Thomas Ballinger wrote: >> I had this problem last Friday with v4.5 cen

[Freesurfer] bbregister

Hi freesurfer-ers: when you run something like: *bbregister --s MySubject --t1 --mov t1_svs.nii --init-fsl --reg t1.reg.dat* ** I expect to generate a file "t1.reg.dat". bbregister is exiting normally with no error message. Where is this file? I cannot find it. Thanks in advance. Saad ___