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
