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):
 
1 DJ301Kit, Mouse, Universal Serial Bus, 2BTN, Optical, Lead Free Black
1MX961Assembly, Card, PERC5I-ADAPTER Serial Attached SCSI
1PD147 Assembly, Cable, Light Emitting Diode, Hard Drive, Auxiliary Precision Workstation, 490
1 PJ058Assembly, Cable, Interface Serial Attached Scsi, Hard Drive, 4, Precision Workstation
1DC740KIT..., SOFTWARE..., RED HAT ENTERPRISE LINUX..., 4WS, PRECISION WORKSTATION..., SUBSCRIPTION..., 1YR, W
1JK141 KIT..., SOFTWARE..., RED HAT ENTERPRISE LINUX..., 4WS, INTEL EXTENDED MEMORY 64 BIT TECHNOLOGY..., MEDIA...
1 RP434Assembly, Floppy Drive 1.44MEGB, Nec Corporation, 05 Black
16GM431Dual In-line Memory Module, 2G 667M, 256X72, 8, 240, 2RX4
1MH366 INSTRUCTION..., DEVIATE CHAS L6 TO L5+
1 XM459Processor, 80563K, Xeon Clovertown, X5355, LGA771, Burn3
4UF070Connector, Serial Attached Scsi, 22P, S, G, INTERPOSER
0149DF INFORMATION..., PREPARATION MATERIAL..., DEVIATION..., PRECISION WORKSTATION..., INCREASE..., #2
1 2R328Cord, Power, 15A, 125V, 5-15/C19
1YN124Assembly, DVD+/-RW..., 16X, IDE Hitachi LG Data Storage, Black
1WH242 Card, Graphics, 256, Fix, 3500 MRGA13
1 TH836Keyboard, 104, UNITED STATES..., MULTI-MEDIA..., Black, LOGITECH...
1XM459Processor, 80563K, Xeon Clovertown, X5355, LGA771, Burn3
1M8034 Hard Drive, 146G, Serial Attached Scsi, 3, 15K, 3.5, FJT AL9L
3 M8034Hard Drive, 146G, Serial Attached Scsi, 3, 15K, 3.5, FJT AL9L
2WG404Assembly, Cable, Serial Ata, HardDrive, Precision Workstation Dozer

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Email:  jkk251@gmail.com





On Wed, Apr 27, 2011 at 5:38 PM, Bruce Fischl <fischl@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



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Cell: 575-571-8274
Email:  jkk251@gmail.com





On Wed, Apr 27, 2011 at 4:52 PM, Bruce Fischl <fischl@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...


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Email:  jkk251@gmail.com



On Mon, Apr 25, 2011 at 12:03 PM, Bruce Fischl
<fischl@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 <
fischl@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 <jkk251@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


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