so tksurfer has never worked for you on any dataset? Have you tried it on one of the ones that we distribute? If it hasn't worked, we'll need to know about your environment (what OS, what video card, are you running in a virtual box, etc...)
cheers Bruce On Wed, 27 Apr 2011, jim kroger wrote: > No, I don't see anything, just black. > Thanks, > Jim > > > > -- > Cell: 575-571-8274 > Email: jkk...@gmail.com > > > > > > On Wed, Apr 27, 2011 at 4:52 PM, Bruce Fischl > <fis...@nmr.mgh.harvard.edu>wrote: > >> and do you see a hemisphere properly rendered or not? >> >> >> On Wed, 27 Apr 2011, jim kroger wrote: >> >> Hi Bruce, this is my first attempt to see something in tksurfer. It's a >>> step >>> in the making edits to white matter. I will go through the tksurfer >>> tutorial, but I noticed that when I start tksurfer, there may be an error. >>> Here's the output, think this might be it? (I am using red hat on a 32 gig >>> Ram pretty fast machine, the drivers should be updated regularly along >>> with >>> all other updates) >>> >>> tksurfer heinrick rh inflated >>> subject is heinrick >>> hemi is rh >>> surface is inflated >>> surfer: current subjects dir: /usr/local/freesurfer/subjects/ >>> surfer: not in "scripts" dir ==> using cwd for session root >>> surfer: session root data dir ($session) set to: >>> surfer: /usr/local/freesurfer/subjects >>> Reading image info (/usr/local/freesurfer/subjects//heinrick) >>> Reading /usr/local/freesurfer/subjects//heinrick/mri/orig.mgz >>> surfer: Reading header info from >>> /usr/local/freesurfer/subjects//heinrick/mri/orig.mgz >>> surfer: vertices=159373, faces=318742 >>> >>> mrisReadTriangleFile(/usr/local/freesurfer/subjects//heinrick/surf/rh.sphere.reg): >>> surface doesn't match >>> /usr/local/freesurfer/subjects//heinrick/surf/rh.inflated >>> >>> mrisReadTriangleFile failed. >>> >>> surfer: single buffered window >>> surfer: tkoInitWindow(heinrick) >>> surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl >>> Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl >>> Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl >>> Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl >>> Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl >>> Successfully parsed tksurfer.tcl >>> reading white matter vertex locations... >>> >>> >>> -- >>> Cell: 575-571-8274 >>> Email: jkk...@gmail.com >>> >>> >>> >>> On Mon, Apr 25, 2011 at 12:03 PM, Bruce Fischl >>> <fis...@nmr.mgh.harvard.edu>wrote: >>> >>> is this in tksurfer? There have been issues with video card drivers, so >>>> make sure your's are up to date. Have you been able to view any surfaces >>>> in >>>> tksurfer? >>>> >>>> >>>> On Mon, 25 Apr 2011, jim kroger wrote: >>>> >>>> HI Bruce, thanks so much for the reply. All of the surfaces we have >>>> needed >>>> >>>>> to view to fix the Talairach (was OK), white matter, etc., have been >>>>> there. >>>>> It's only when I tried to look at the inflated brain during the >>>>> WhiteMatterEdits >>>>> step that something seemed to be missing. I will look at tkmedit and >>>>> tkregister2 documentation to see if there are different ways to look for >>>>> the >>>>> inflated brain, but if anybody has suggestions on why I'm seeing only a >>>>> tiny >>>>> fraction it would be great. It sort of seems like a thresholding issue, >>>>> but >>>>> I have no idea why on little 2 square inch or so section of cortex is >>>>> there >>>>> and the rest is not, or I can't see it. The edges of what I see are very >>>>> sharp and defined. >>>>> >>>>> Jim >>>>> >>>>> >>>>> >>>>> On Sat, Apr 23, 2011 at 9:16 PM, Bruce Fischl < >>>>> fis...@nmr.mgh.harvard.edu >>>>> >>>>>> wrote: >>>>>> >>>>> >>>>> Hi Jim >>>>> >>>>>> Have you been able to view other surfaces in tksurfer? The situation >>>>>> you >>>>>> describe sounds normal except for the display issue (e.g. The thalamus >>>>>> should be interior to the white surface) >>>>>> Cheers >>>>>> Bruce >>>>>> >>>>>> >>>>>> >>>>>> On Apr 22, 2011, at 12:28 PM, jim kroger <jkk...@gmail.com> wrote: >>>>>> >>>>>> Hello, I am following the sequence in the "FreeSurfer Troubleshooting >>>>>> Reconstruction Work Flow" instructions, and am at step 8, >>>>>> FsTutorial/WhiteMatterEdits. It looks like the thalamus and corpus >>>>>> callosum >>>>>> are included as white matter, and the pial surface surrounds some >>>>>> subcortical structures. Assuming this is not correct, I decided to look >>>>>> at >>>>>> the inflated surface as suggested in the referenced page " Making Edits >>>>>> to >>>>>> the White Matter." Unfortunately when I issue: >>>>>> >>>>>> tksurfer wm1_edits_before rh inflated >>>>>> >>>>>> I only see what looks like a very small fraction of an egg shell for >>>>>> the >>>>>> rh, and nothing for lh. Can I check somehow to see why I have almost no >>>>>> inflated brain? >>>>>> >>>>>> Thanks, >>>>>> Jim >>>>>> >>>>>> >>>>>> -- >>>>>> Cell: 575-571-8274 >>>>>> Email: <jkk...@gmail.com>jkk...@gmail.com >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> >>>>>> The information in this e-mail is intended only for the person to whom >>>>>> it >>>>>> is >>>>>> addressed. If you believe this e-mail was sent to you in error and the >>>>>> e-mail >>>>>> contains patient information, please contact the Partners Compliance >>>>>> HelpLine at >>>>>> http://www.partners.org/complianceline . If the e-mail was sent to you >>>>>> in >>>>>> error >>>>>> but does not contain patient information, please contact the sender and >>>>>> properly >>>>>> dispose of the e-mail. >>>>>> >>>>>> >>>>>> >>>>> >>> > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
