Freesurfer

freesurfer@nmr.mgh.harvard.edu

4 participants
30076 discussions

Changing the color in Edit Segmentation tool
by Jared Conley 18 May '07

18 May '07

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 Main Toolbar, by choosing *Tools->Edit Segmentation*, or by pressing the 'g' key. By clicking with button 2 with this tool, you can 'paint' a label in the segmentation. The color used can be set in the dialog box brought up by choosing *Tools->Configure Segmentation Brush....* However, I am not able to change the color to match the structure I am wanting to edit (I have tried selecting three different structures at random and the color of the editing remains grey). Any ideas? Jared FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-tiger-i686-stable-pub-v3.0.5 Kernel info: Darwin 8.9.1 i386 ---------------------------------------------------------------------

3 9

Re: [Freesurfer] recon-all exited with ERRORS
by Jenni Pacheco 18 May '07

18 May '07

Hi Annie, The aparc+aseg has the aseg subcortical labels in the wm regions, and has the parcellation labels along the cortex. This is overlaid on volumes in tkmedit. A description and a snapshot is shown at the bottom of this page: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData Jenni On Fri, 18 May 2007, Annie Chiu wrote: > Hi Jenni, > > Thanks very much for your speedy reply. Before understanding whether I need > aparc+aseg, could you let me know what the file entails? > > Thanks again, > Annie > > On 5/17/07 5:48 PM, "Jenni Pacheco" <jpacheco(a)nmr.mgh.harvard.edu> wrote: > >> Hi Annie, >> >> I think what's happening is that it's failing in the aparc+aseg step, but >> you can verify this by looking at the status log in your subjects >> scripts/recon-all-status.log >> >> This step uses some previously generated input to make a new segmentation. >> The lh.ribbon.mgz is a newer addition to the recon-all stream, currently >> run in autorecon2. If your data is old it may not have this, and so the >> aparc+aseg can not be generated. You can either survive without the >> aparc+aseg if you don't want it, or you can generate the ?h.ribbon.mgz by >> running >> recon-all -cortribbon -s <subjid> and then trying recon-all -aparc2aseg -s >> <subjid> >> >> But first, do verify with the status log that this is the step thats >> failing! >> >> Jenni >> >> On Thu, 17 May 2007, Chiu, Annie (NIH/NINDS) [F] wrote: >> >>> Hello all, >>> >>> Using the most updated version of freesurfer, I ran autorecon3 on a set of >>> data obtained with an old version of the software (the first version) and I >>> obtained the following error message: >>> >>> Loading rh annotations from >>> /home/chiuan/freesurfer/subjects/becker2ANNIE/label/rh.aparc.annot >>> Have color table for lh white annotation >>> Have color table for rh white annotation >>> Loading lh ribbon mask from >>> /home/chiuan/freesurfer/subjects/becker2ANNIE/mri/lh.ribbon.mgz >>> ERROR: loading aseg >>> /home/chiuan/freesurfer/subjects/becker2ANNIE/mri/lh.ribbon.mgz >>> Linux mushrat.ninds.nih.gov 2.6.9-42.0.2.ELsmp #1 SMP Thu Aug 17 18:00:32 EDT >>> 2006 i686 i686 i386 GNU/Linux >>> >>> recon-all exited with ERRORS at Wed May 16 22:24:13 EDT 2007 >>> >>> Could someone please clarify? >>> >>> Thanks in advance, >>> Annie >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> > > >

1 0

probabilistic labels
by Wanmei Ou 18 May '07

18 May '07

Hi, Is there a way to get probabilistic labels for ?h.sphere.reg? If I understand it right, mris_ca_label oand mris_divide_parcellation only return the MAP solution of the probabilistic labels. Thanks, Wanmei

2 1

recon-all exited with ERRORS
by Chiu, Annie (NIH/NINDS) [F] 17 May '07

17 May '07

Hello all, Using the most updated version of freesurfer, I ran autorecon3 on a set of data obtained with an old version of the software (the first version) and I obtained the following error message: Loading rh annotations from /home/chiuan/freesurfer/subjects/becker2ANNIE/label/rh.aparc.annot Have color table for lh white annotation Have color table for rh white annotation Loading lh ribbon mask from /home/chiuan/freesurfer/subjects/becker2ANNIE/mri/lh.ribbon.mgz ERROR: loading aseg /home/chiuan/freesurfer/subjects/becker2ANNIE/mri/lh.ribbon.mgz Linux mushrat.ninds.nih.gov 2.6.9-42.0.2.ELsmp #1 SMP Thu Aug 17 18:00:32 EDT 2006 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Wed May 16 22:24:13 EDT 2007 Could someone please clarify? Thanks in advance, Annie

2 1

tkmedit
by Martin Chang 17 May '07

17 May '07

>Hi, > >I have a question about using tkmedit. Up until now, our group has been >editing out the eye muscles after autorecon-1 and editing out the optic >nerve after autorecon-2. I know on earlier versions of freesurfer it was >highly recommended to do so because the program would sometimes crash >otherwise. However, using the newer version, the program seems to know to >not include eye muscles in the pial matter boundary, and the optic nerve >does create a region of high curvature at that point, but it doesn't crash >the program. > >I was wondering, in your own analyses, did you do editing at each step >(excluding situations that are obviously out of the norm), and would it be >a bad thing not to edit those regions in the majority of cases? > >Thanks, >Martin Chang _________________________________________________________________ PC Magazines 2007 editors choice for best Web mailaward-winning Windows Live Hotmail. http://imagine-windowslive.com/hotmail/?locale=en-us&ocid=TXT_TAGHM_migrati…

2 1

Temporal derivative in mkanalysis-sess
by Dan Dillon 16 May '07

16 May '07

Dear FreeSurfers, I'd like to add a temporal derivative to my gammafit model and understand that this can be done using mkanalysis-sess. However, I can't seem to track down the relevant flag (using -help or the wiki). Can someone point me in the right direction? Thanks! Dan Dillon

2 1

Grey matter issue.
by Kt Labadie 16 May '07

16 May '07

Hello. I have attached an image of a case I am working that I can't figure out how to fix. I have approximately 15 cases like this, so any suggestions would be helpful. You can see that some grey matter is not being included along the left and right sides. It is like this for about 30 slides. I did a few things to try and fix it, but nothing worked. I adjusted the watershed number to 30 and it just included the entire skull and did not expand the surface out. I also used the -atlas and -more commands to try and adjust the surface, but it did not shift. I also checked the Talairach registration, but it was fine. Any suggestions? Thanks KT LaBadie Research Associate The Mind Institute

1 0

Re: [Freesurfer] Editing Segmentation Results in TkMedit
by Jared Conley 16 May '07

16 May '07

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" 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. I have tried running the command >>>> "tkmedit subjid wm.mgz -aux T1.mgz" as directed, but it gives me an >>>> error. Could someone direct me to the correct tutorial or answer >>>> my question directly. Thanks. >>>> >>>> Jared >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >> X11 terminal says "Error: Loading volume ... couldn't read the >> anatomical volume." I am worried that perhaps it's due to my >> SUBJECTS_DIR environment variable not being properly set, as >> indicated in the Wiki. Let me know what you think. >> >> >> It is working now. Thanks for the assistance.

1 0

Editing Segmentation Results in TkMedit
by Jared Conley 16 May '07

16 May '07

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. I have tried running the command "tkmedit subjid wm.mgz -aux T1.mgz" as directed, but it gives me an error. Could someone direct me to the correct tutorial or answer my question directly. Thanks. Jared

2 1

(no subject)
by Bagnato, Francesca (NIH/NINDS) [E] 16 May '07

16 May '07

Can I open images parcellated with an old version of freesurfer (the one parcellating 80 regions) with the new one (based upon the Desikan atals)? Thanks, Francesca Francesca Bagnato, MD-PhD Staff Scientist, NIB-NINDS-NIH Building 10, Room 5S205 9000 Rockville Pike Bethesda, MD, 20892-1400 MSC Phone #: (301) 594-1415 Fax #: (301) 402-0373

2 10

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer