Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

make_average_subject
by Furlong, Carolyn 21 May '07

21 May '07

Hi, I'm still having problems with make_average_subject, when I type the folowing command line in: >make_average_subject --debug --subjects 'subject1' 'subject2'..... --out PLP_average --no-symlink echo ERROR: Flag $flag unrecognized. echo ERROR: Flag --no-symlink unrecognized. ERROR: Flag --no-symlink unrecognized. echo $cmdline echo ....... exit 1 exit 1 and when I try to view the results by > tksurfer PLP_average lh inflated I get the message: surfer: current subjects dir: /disc2/Kate/Flatmap1 surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /disc2/Kate/Flatmap1 surfer: ### Could not find anatomical header information. The mri folder does not contain the same files that the tutorial example subject 'buckner fsaverage' does, what do you think is going wrong? Thanks for your help Best wishes Carolyn

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reg -feat2anat error
by Furlong, Carolyn 21 May '07

21 May '07

Hi Doug Please find attached the logfile that you requested, sorry for the delay, I am only able to work on this one day a week. Best wishes Carolyn Actually, I wanted the log file found in featdir/reg/freesurfer/reg-feat2anat.log. doug Furlong, Carolyn wrote: > Hi > > > niiRead(): unsupported timing pattern in Pre_DB/DB_Prelip_BET.feat/example_func.nii.gz > > sorry for the delay, > > Best wishes > > Carolyn > > can you send the log file? > > Furlong, Carolyn wrote: > >> Hi, >> >> When I try to register my functional data to anatomical data using >> >> reg-feat2anat --feat feat_directory --subject subject_name >> >> I get the following error message >> >> ERROR: could not read ///example_func.nii.gz as 24 >> >> What does this mean? And how can I fix this? >> >> Best wishes >> Carolyn >> >> >>_______________________________________________ >>Freesurfer mailing list >>Freesurfer(a)nmr.mgh.harvard.edu >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >greve(a)nmr.mgh.harvard.edu >Phone Number: 617-724-2358 >Fax: 617-726-7422 > >In order to help us help you, please follow the steps in: >surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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RE: [Freesurfer] tkmedit
by Jenni Pacheco 21 May '07

21 May '07

Hi Martin, You should be fine not editing these regions routinely - only, of course, if they pose a problem for your surfaces. For the most part, also, you should be fine to run the entire stream and do any edits that may be needed after the fact - instead of running stepwise and checking each output along the way. Jenni -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Martin Chang Sent: Thursday, May 17, 2007 12:34 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] tkmedit >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 Magazine's 2007 editors' choice for best Web mail-award-winning Windows Live Hotmail. http://imagine-windowslive.com/hotmail/?locale=en-us&ocid=TXT_TAGHM_migratio n_HM_mini_pcmag_0507 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Where to get mri_binarize?
by Dan Dillon 18 May '07

18 May '07

I would like to use mri_binarize but don't seem to have it (running stable 3.0.3). Where can I get it? Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 496-5222 E-mail: dillon(a)wjh.harvard.edu

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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 ---------------------------------------------------------------------

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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 >>> >>> >>> > > >

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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

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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

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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…

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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

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