Hi Bruce, returning back to this. I tried the same command on the tutorial data set (bert):
tksurfer bert rh inflated and I did not get the error about rh.sphere.reg surface not matching rh.inflated that I got with my data, but I still have the same problem with the tutorial data (bert). I see only a tiny part of the inflated brain in tksurfer. I have not tried to use tksurfer except to look at the inflated brain (my data then bert). For example if we were looking at an egg, I would only see one little piece of the shell, maybe 10% of the whole shell. Not sure what to do next. Since this happens with the tutorial data, I'll give you the info you indicated: Graphics card: Dell WH242 Nvidia Quadro FX 3500, 256MB, Dual DVI Out, PCIe x16, MRGA13 CRD,GRPHC,256,FX, OS: Running Red Hat Enterprise 5, which auto updates so I would think I have the latest drivers I access this machine remotely using NX from a Dell Precision T5500 running Win7 64. Here are the rest of the machine specs in case they are helpful (except have upgraded to red hat 5): 1DJ301Kit, Mouse, Universal Serial Bus, 2BTN, Optical, Lead Free Black1MX961Assembly, Card, PERC5I-ADAPTER Serial Attached SCSI1PD147Assembly, Cable, Light Emitting Diode, Hard Drive, Auxiliary Precision Workstation, 4901PJ058Assembly, Cable, Interface Serial Attached Scsi, Hard Drive, 4, Precision Workstation1 DC740KIT..., SOFTWARE..., RED HAT ENTERPRISE LINUX..., 4WS, PRECISION WORKSTATION..., SUBSCRIPTION..., 1YR, W1JK141KIT..., SOFTWARE..., RED HAT ENTERPRISE LINUX..., 4WS, INTEL EXTENDED MEMORY 64 BIT TECHNOLOGY..., MEDIA...1RP434Assembly, Floppy Drive 1.44MEGB, Nec Corporation, 05 Black16 GM431Dual In-line Memory Module, 2G 667M, 256X72, 8, 240, 2RX41MH366INSTRUCTION..., DEVIATE CHAS L6 TO L5+1XM459Processor, 80563K, Xeon Clovertown, X5355, LGA771, Burn34UF070Connector, Serial Attached Scsi, 22P, S, G, INTERPOSER0 149DFINFORMATION..., PREPARATION MATERIAL..., DEVIATION..., PRECISION WORKSTATION..., INCREASE..., #212R328Cord, Power, 15A, 125V, 5-15/C191YN124Assembly, DVD+/-RW..., 16X, IDE Hitachi LG Data Storage, Black1WH242Card, Graphics, 256, Fix, 3500 MRGA131TH836Keyboard, 104, UNITED STATES..., MULTI-MEDIA..., Black, LOGITECH...1XM459Processor, 80563K, Xeon Clovertown, X5355, LGA771, Burn31M8034Hard Drive, 146G, Serial Attached Scsi, 3, 15K, 3.5, FJT AL9L3 M8034Hard Drive, 146G, Serial Attached Scsi, 3, 15K, 3.5, FJT AL9L2WG404Assembly, Cable, Serial Ata, HardDrive, Precision Workstation Dozer -- 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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