Re: [Freesurfer] ICV accuracy

Thanks, Bruce. That seemed to work well. Jared -- Jared Conley Center for Neurological Imaging Brigham and Women's Hospital Harvard Medical School 221 Longwood Ave., RF 394 P: 617.525.6238 Bruce Fischl wrote: Hi Jared, you can load the source (nu_noneck.mgz) and target (/autofs/

[Freesurfer] ICV accuracy

FreeSurfer Community: A quick question for the group. Our lab was wondering if there is an easy way to assess the accuracy of the intracranial volume (ICV) measurement? Or is this not necessary (never any errors)? Thanks in advance, Jared -- Jared Conley Center for Neurological Imaging

Re: [Freesurfer] Aseg.stats file

Thanks. That seemed to work just fine. Jared Bruce Fischl wrote: I think recon-all -subjid -segstats should do itOn Wed, 30 Jan 2008, Jared Conley wrote: FreeSurfer Community, Is there an easy, quick way to regenerate the aseg.stats file? This particular file was deleted accidentally

[Freesurfer] Aseg.stats file

FreeSurfer Community, Is there an easy, quick way to regenerate the aseg.stats file? This particular file was deleted accidentally for a few subjects and we wondered if we could quickly recreate this file without having to run recon-all again. All the other files in the subject directory are

[Freesurfer] Neuroimaging Research Position Available

in an HIV cohort and a separate aging cohort. A candidate with FreeSurfer/FSL experience will have a distinct advantage (but is not requisite). If interested please respond with your CV attached. Thanks, Jared -- Jared Conley Department of Radiology/Neurology Brigham and Women's Hospit

Re: [Freesurfer] Manually editing brainmask.mgz

its to the brainmask - but I'd guess the surfaces won't be accurate, some things may not run at all. Jenni On Mon, 11 Jun 2007, Jared Conley wrote: Jenni, Another question for you. What is the consequence of running autorecon2 after editing on the brainmask.mgz file itself. You mentione

Re: [Freesurfer] Manually editing brainmask.mgz

nd if you eventually want to use Freesurfer to obtain surfaces etc, this will not work. I'd suggest saving your brainmask as something else, and edit that - this way you still have a viable brainmask.mgz to obtain results with. Jenni On Mon, 11 Jun 2007, Jared Conley wrote: Hi Jenni, I am

Re: [Freesurfer] Manually editing brainmask.mgz

thing else, and edit that - this way you still have a viable brainmask.mgz to obtain results with. Jenni On Mon, 11 Jun 2007, Jared Conley wrote: Hi Jenni, I am trying to edit the greyscale images of the brainmask.mgz. We are trying to generate an ICC map with only grey/white matter and w

Re: [Freesurfer] Manually editing brainmask.mgz

need a little bit more information on what you are doing and what is going wrong. Thanks, Jenni On Mon, 11 Jun 2007, Jared Conley wrote: FreeSurfer community, I am attempting to manually edit brainmask.mgz in TkMedit and cannot figured out how to do so based on the info in the Wiki. I lo

[Freesurfer] Manually editing brainmask.mgz

FreeSurfer community, I am attempting to manually edit brainmask.mgz in TkMedit and cannot figured out how to do so based on the info in the Wiki. I load the file in X11 with the command and see the images just fine, but I cannot seem to manually edit them like I can in the segmentation fil

Re: [Freesurfer] Changing the color in Edit Segmentation tool

Jenni Pacheco wrote: When you are editing the segmentation, are you using the middle button to change the label? jenni On Fri, 18 May 2007, Jared Conley wrote: Jenni Pacheco wrote: Hi Jared, How are you selecting the segmentation that you wish to be changing it to? Have you opened the

Re: [Freesurfer] Changing the color in Edit Segmentation tool

Jenni Pacheco wrote: Hi Jared, How are you selecting the segmentation that you wish to be changing it to? Have you opened the Segmentation Bruch Info dialog window and selected from the list in there? jenni On Fri, 18 May 2007, Jared Conley wrote: In response to the questions, I do see

Re: [Freesurfer] Changing the color in Edit Segmentation tool

e over the edited voxels and verify that the values in the "Sgmtn label" line in the tools window matches the value you selected in the Segmentation Brush Info dialog? On Thu, May 17, 2007 at 02:56:57PM -0400, Jared Conley wrote: Yes, I believe so. The layer's color map is set t

Re: [Freesurfer] Changing the color in Edit Segmentation tool

Kevin Teich wrote: Are you sure the Target Layer is set to the segmentation volume layer? And that that layer's color map type is set to LUT? On Thu, May 17, 2007 at 11:23:49AM -0400, Jared Conley wrote: I am attempting to edit the segmentation results in TkMedit, according to the

[Freesurfer] Changing the color in Edit Segmentation tool

I am attempting to edit the segmentation results in TkMedit, according to the following Wiki directions ( > TkMeditGuide/TkMeditWorkingWithData/TkMeditSegmentations): A segmentation can be edited with the Edit Segmentation tool, which can be activated by pushing the icon_copy.gif button on the M

Re: [Freesurfer] Editing Segmentation Results in TkMedit

Bruce Fischl wrote: could be. Is it set to the right place? On Wed, 16 May 2007, Jared Conley wrote: Bruce Fischl wrote: what is the error? On Wed, 16 May 2007, Jared Conley wrote: I am new to FreeSurfer and am attempting to segment T1 images using the "recon-all...autorecon2&quo

[Freesurfer] Editing Segmentation Results in TkMedit

I am new to FreeSurfer and am attempting to segment T1 images using the "recon-all...autorecon2" command. The segmentation results look quite accurate, but I was wondering how to best edit the results (where there is a need). I noticed on the Wiki a possible option using the TkMedit program.

[Freesurfer] Editing Segmentation Results

I am new to FreeSurfer and am attempting to segment T1 images using the "recon-all...autorecon2" command. The segmentation results look quite accurate, but I was wondering how to best edit the results (where there is a need). I noticed on the Wiki a possible option using I think either 3D Sli