Great idea, I didn't try this on the tutorial data set. Will let you know. Jim
-- Cell: 575-571-8274 Email: jkk...@gmail.com On Wed, Apr 27, 2011 at 5:38 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > 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. >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>> >>
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