[Freesurfer] sulc

Dear freesurfers, i m running an analysis using qdec trying to find the group difference between healthy subjects and MCIs according to their sulc parameter. My question is, is there an output file with the statistics results as text file and if so can u please tell me where is it located?? my

[Freesurfer] mesh size question

Hi all, I'm using the mri_watershed instruction to extract the skull and skin mesh, because I'm using them in a boundary element method, but the dimensions of these meshes are too big for my application (20480 faces and 10242 vertices for each ones). Do you know if there is a way to define a

Re: [Freesurfer] mesh size question

Hi Tommaso, I am not sure about freesurfer, but why don't you simply use a standard tool for mesh simplification e.g. qslim http://graphics.cs.uiuc.edu/~garland/software/qslim.html probably there are more. Martin On Wed, 2008-10-22 at 14:48 +0200, Tommaso De Marco wrote: > Hi all, > I'm using t

[Freesurfer] failure of qdec

I'm running stable version of freesurfer 4.05 on 64 bit ubuntu 7.10. Every time when I tried to run the qdec, it generated the error message below. Reading /apps/freesurfer/freesurfer/lib/tcl/tkUtils.tcl Using /apps/freesurfer/freesurfer/lib/tcl/fsgdfPlot.tcl X Error of failed request: BadMatc

Re: [Freesurfer] failure of qdec

Lan, Try adding this to the end of your /etc/X11/xorg.conf file: Section "Extensions" Option "Composite" "false" EndSection You will need to reboot your X11 server after doing so. Nick > I'm running stable version of freesurfer 4.05 on 64 bit ubuntu 7.10. > Every time when I tried to run

Re: [Freesurfer] sulc

David, qdec output data is found in your $SUBJECTS_DIR/qdec directory. It is not in text format, as it is per-vertex data. The file 'sig.mgh' is the main significance result file. mris_convert can be used to convert that to text format if you need values at each vertex. Nick > > Dear freesurf

[Freesurfer] FreeSurferColorLUT & aparc

Hi, Running fsv405 on RHEL5. I've encountered some unexpected numerical values wrt FreeSurferColorLUT.txt. Are my expectations off? 1) In the aparc+aseg.mgz file, intensity values for the cortical labels range from -32768 to 654, with negative values falling in some regions in the left hemisphe

Re: [Freesurfer] FreeSurferColorLUT & aparc

Hi Jenifer, how are you getting those intensity values? Bruce On Wed, 22 Oct 2008, Juranek, Jenifer wrote: Hi, Running fsv405 on RHEL5. I've encountered some unexpected numerical values wrt FreeSurferColorLUT.txt. Are my expectations off? 1) In the aparc+aseg.mgz file, intensity values f

RE: [Freesurfer] FreeSurferColorLUT & aparc

I'm able to view the intensity values in FSL. Is there another approach I can take to doublecheck? Jenifer -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Wednesday, October 22, 2008 4:15 PM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Frees

RE: [Freesurfer] FreeSurferColorLUT & aparc

if you load it in tkmedit is it displayed properly? On Wed, 22 Oct 2008, Juranek, Jenifer wrote: I'm able to view the intensity values in FSL. Is there another approach I can take to doublecheck? Jenifer -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Wednesday

RE: [Freesurfer] FreeSurferColorLUT & aparc

yes, the correct Sgmtn label is displayed in the TkMedit Tools -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Wednesday, October 22, 2008 4:30 PM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] FreeSurferColorLUT & aparc if you lo

[Freesurfer] Error with mri_convert failing to write orig/001.mgz

Hey everyone, I'm having some issues trying to run the volume pipeline using .BRIK input from afni (hence running mri_convert command directly). The problem occurs at the end of mri_convert at the very beginning when Freesurfer fails to write orig/001.mgz, and I'm not sure if I'm making a mistake

Re: [Freesurfer] Error with mri_convert failing to write orig/001.mgz

Hi John, can you send us the command line you are running? cheers, Bruce On Wed, 22 Oct 2008, John Sheppard wrote: Hey everyone, I'm having some issues trying to run the volume pipeline using .BRIK input from afni (hence running mri_convert command directly). The problem occurs at the end

Re: [Freesurfer] Error with mri_convert failing to write orig/001.mgz

Hey Bruce, Here's the command line I'm using - sorry realized I should've included it after sending the email: It just goes to the subject folder ($subject-$scan) and then does it's thing - already in tcsh shell with all the environment variables set and the .csh file sourced. Volume_ns+orig.BRIK