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. >>>>> >>>>> >>>>> >>>> >>
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