Re: segmentation

2003-06-04 Thread L . Scheef
Hi Kevin, I agree with Bruce. It sounds like a BIAS field problem. You might want to use FAST from the FSL-package to solve the problem (http://www.fmrib.ox.ac.uk/fsl/fast/) or the matlab script from http://www.psych.stanford.edu/~kalina/SPM99/Tools/vol_homocor.html Good luck! Lukas Date sent

Re: segmentation

2003-06-04 Thread Bruce Fischl
Hi Kevin, this sounds like a bias field problem. You can try manually selecting some control points in tkmedit near the calcarine, but make sure that the ones you pick are not partial-volumed (they must be completely within the white matter). Also, you want to pick ones that are below the inten

segmentation

2003-06-04 Thread Kevin H.
ok thanks doug also, i'm having trouble segmenting the white matter in the visual cortex. (its too dark, almost as bright as the grey matter in the mid brain) we've averaged multiple scans but that doesn't seem to help. would changing the normalization parameters in the Expert preferences help?

Re: registration

2003-06-04 Thread Doug Greve
Try using tkregister2 instead. Run with --help to get more info. doug "Kevin H." wrote: > > hello, > > how do i register a 2d anatomical scan (same session as fmri scan) to a > 3d anatomical scan? I've tried using tkregister, but it seems that it > is only for registering fmri scans onto the 3

registration

2003-06-04 Thread Kevin H.
hello, how do i register a 2d anatomical scan (same session as fmri scan) to a 3d anatomical scan? I've tried using tkregister, but it seems that it is only for registering fmri scans onto the 3d scans. It is difficult to register the functional and anatomical scans since only a part of the br

Re: Mac installation

2003-06-04 Thread gamal akabani hneide
On 6/3/03 2:34 PM, "Doug Greve" <[EMAIL PROTECTED]> wrote: > gamal akabani hneide wrote: >> > >> Also, what are the commonalities between fsl and freesurfer? > > We've set it up so that an fsl registration matrix can be easily > converted into something that freesurfer can understand (ie, a > r

Re: Mac installation

2003-06-04 Thread Doug Greve
gamal akabani hneide wrote: > > Also, what are the commonalities between fsl and freesurfer? We've set it up so that an fsl registration matrix can be easily converted into something that freesurfer can understand (ie, a register.dat file); this is done with tkregister2. You can also resample th

Re: pial surf problem?

2003-06-04 Thread Bruce Fischl
Hi Mark, it looks like the pial surface is extending too far. When mris_make_surfaces starts it prints out a bunch of information about detected intentis limits. The interesting ones for your purposes will be max_gray_at_csf_border, min_gray_at_csf_border, and max_csf. It seems like it thinks

Re: new version of freesurfer

2003-06-04 Thread Kevin Teich
> is the new version out yet? or is it still on hold Still on hold. -- Kevin Teich

new version of freesurfer

2003-06-04 Thread Andy Myers
sorry, is the new version out yet? or is it still on hold thanks andy

Re: Mac installation

2003-06-04 Thread Vicka Corey
On Tue, Jun 03, 2003 at 12:26:32AM -0400, gamal akabani hneide wrote: > Hi all, > > I am trying to install freesurfer on a mac. However, the instructions are > not very clear in the INSTALL file as many directories are not generated > when I tar xvfz the unloaded file. Are there any specific instr