When I run tksurfer, only portions of the cuneus, lateral occipital, and superior parietal regions are displayed. This occurs in both FS versions 4.2.0 and 4.4.0. I am using a 32 bit BU Linux system which is equivalent to redhat 5.0. The error message is similar to those in previous posts, but previous suggestions don't seem to help.
surfer: current subjects dir: /home/freesurfer4.2.0/subjects/corinna/PET surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/freesurfer4.2.0/subjects/corinna/PET surfer: Reading header info from /home/freesurfer4.2.0/subjects/corinna/PET/003_S_1059/mri/T1.mgz surfer: vertices=119899, faces=239794 Loading /home/freesurfer4.2.0/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(003_S_1059) surfer: using interface /home/freesurfer4.2.0/lib/tcl/tksurfer.tcl Reading /home/freesurfer4.2.0/lib/tcl/tkm_common.tcl Reading /home/freesurfer4.2.0/lib/tcl/tkm_wrappers.tcl Reading /home/freesurfer4.2.0/lib/tcl/fsgdfPlot.tcl Reading /home/freesurfer4.2.0/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations...
try: setenv doublebufferflag 1
before running tksurfer ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br --- Em breve Netfilter Small Business
2009/8/10 corinna bauer corinnab83@gmail.com
When I run tksurfer, only portions of the cuneus, lateral occipital, and superior parietal regions are displayed. This occurs in both FS versions 4.2.0 and 4.4.0. I am using a 32 bit BU Linux system which is equivalent to redhat 5.0. The error message is similar to those in previous posts, but previous suggestions don't seem to help.
surfer: current subjects dir: /home/freesurfer4.2.0/subjects/corinna/PET surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/freesurfer4.2.0/subjects/corinna/PET surfer: Reading header info from /home/freesurfer4.2.0/subjects/corinna/PET/003_S_1059/mri/T1.mgz surfer: vertices=119899, faces=239794 Loading /home/freesurfer4.2.0/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(003_S_1059) surfer: using interface /home/freesurfer4.2.0/lib/tcl/tksurfer.tcl Reading /home/freesurfer4.2.0/lib/tcl/tkm_common.tcl Reading /home/freesurfer4.2.0/lib/tcl/tkm_wrappers.tcl Reading /home/freesurfer4.2.0/lib/tcl/fsgdfPlot.tcl Reading /home/freesurfer4.2.0/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
That didn't work. Corinna
2009/8/10 Pedro Paulo de Magalhães Oliveira Junior ppj@netfilter.com.br
try: setenv doublebufferflag 1
before running tksurfer
Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br --- Em breve Netfilter Small Business
2009/8/10 corinna bauer corinnab83@gmail.com
When I run tksurfer, only portions of the cuneus, lateral occipital, and superior parietal regions are displayed. This occurs in both FS versions 4.2.0 and 4.4.0. I am using a 32 bit BU Linux system which is equivalent to redhat 5.0. The error message is similar to those in previous posts, but previous suggestions don't seem to help.
surfer: current subjects dir: /home/freesurfer4.2.0/subjects/corinna/PET surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/freesurfer4.2.0/subjects/corinna/PET surfer: Reading header info from /home/freesurfer4.2.0/subjects/corinna/PET/003_S_1059/mri/T1.mgz surfer: vertices=119899, faces=239794 Loading /home/freesurfer4.2.0/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(003_S_1059) surfer: using interface /home/freesurfer4.2.0/lib/tcl/tksurfer.tcl Reading /home/freesurfer4.2.0/lib/tcl/tkm_common.tcl Reading /home/freesurfer4.2.0/lib/tcl/tkm_wrappers.tcl Reading /home/freesurfer4.2.0/lib/tcl/fsgdfPlot.tcl Reading /home/freesurfer4.2.0/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Can you post the output of dmesg command ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br --- Em breve Netfilter Small Business
2009/8/10 corinna bauer corinnab83@gmail.com
That didn't work. Corinna
2009/8/10 Pedro Paulo de Magalhães Oliveira Junior ppj@netfilter.com.br
try:
setenv doublebufferflag 1
before running tksurfer
Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br --- Em breve Netfilter Small Business
2009/8/10 corinna bauer corinnab83@gmail.com
When I run tksurfer, only portions of the cuneus, lateral occipital, and superior parietal regions are displayed. This occurs in both FS versions 4.2.0 and 4.4.0. I am using a 32 bit BU Linux system which is equivalent to redhat 5.0. The error message is similar to those in previous posts, but previous suggestions don't seem to help.
surfer: current subjects dir: /home/freesurfer4.2.0/subjects/corinna/PET surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/freesurfer4.2.0/subjects/corinna/PET surfer: Reading header info from /home/freesurfer4.2.0/subjects/corinna/PET/003_S_1059/mri/T1.mgz surfer: vertices=119899, faces=239794 Loading /home/freesurfer4.2.0/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(003_S_1059) surfer: using interface /home/freesurfer4.2.0/lib/tcl/tksurfer.tcl Reading /home/freesurfer4.2.0/lib/tcl/tkm_common.tcl Reading /home/freesurfer4.2.0/lib/tcl/tkm_wrappers.tcl Reading /home/freesurfer4.2.0/lib/tcl/fsgdfPlot.tcl Reading /home/freesurfer4.2.0/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The output from dmesg is:
Linux version 2.6.18-128.1.14.el5 (mockbuild@builder16.centos.org) (gcc version 4.1.2 20080704 (Red Hat 4.1.2-44)) #1 SMP Wed Jun 17 06:40:54 EDT 2009 BIOS-provided physical RAM map: BIOS-e820: 0000000000000000 - 000000000009b800 (usable) BIOS-e820: 000000000009b800 - 00000000000a0000 (reserved) BIOS-e820: 00000000000e0000 - 0000000000100000 (reserved) BIOS-e820: 0000000000100000 - 000000003ff70000 (usable) BIOS-e820: 000000003ff70000 - 000000003ff7b000 (ACPI data) BIOS-e820: 000000003ff7b000 - 000000003ff80000 (ACPI NVS) BIOS-e820: 000000003ff80000 - 0000000040000000 (reserved) BIOS-e820: 00000000fec00000 - 00000000fec10000 (reserved) BIOS-e820: 00000000fee00000 - 00000000fee01000 (reserved) BIOS-e820: 00000000ff800000 - 00000000ffc00000 (reserved) BIOS-e820: 00000000fff00000 - 0000000100000000 (reserved) 127MB HIGHMEM available. 896MB LOWMEM available. found SMP MP-table at 000f6120 Memory for crash kernel (0x0 to 0x0) notwithin permissible range disabling kdump Using x86 segment limits to approximate NX protection On node 0 totalpages: 262000 DMA zone: 4096 pages, LIFO batch:0 Normal zone: 225280 pages, LIFO batch:31 HighMem zone: 32624 pages, LIFO batch:7 DMI present. Using APIC driver default ACPI: RSDP (v000 PTLTD ) @ 0x000f6160 ACPI: RSDT (v001 PTLTD RSDT 0x06040000 LTP 0x00000000) @ 0x3ff76ee4 ACPI: FADT (v001 INTEL E7505 0x06040000 PTL 0x00000008) @ 0x3ff7ae78 ACPI: MADT (v001 PTLTD APIC 0x06040000 LTP 0x00000000) @ 0x3ff7aeec ACPI: BOOT (v001 PTLTD $SBFTBL$ 0x06040000 LTP 0x00000001) @ 0x3ff7af88 ACPI: SPCR (v001 PTLTD $UCRTBL$ 0x06040000 PTL 0x00000001) @ 0x3ff7afb0 ACPI: DSDT (v001 INTEL E7505 0x06040000 MSFT 0x0100000e) @ 0x00000000 ACPI: PM-Timer IO Port: 0x1008 ACPI: Local APIC address 0xfee00000 ACPI: LAPIC (acpi_id[0x00] lapic_id[0x00] enabled) Processor #0 15:2 APIC version 20 ACPI: LAPIC (acpi_id[0x01] lapic_id[0x06] enabled) Processor #6 15:2 APIC version 20 ACPI: LAPIC (acpi_id[0x02] lapic_id[0x01] enabled) Processor #1 15:2 APIC version 20 ACPI: LAPIC (acpi_id[0x03] lapic_id[0x07] enabled) Processor #7 15:2 APIC version 20 ACPI: LAPIC_NMI (acpi_id[0x00] high edge lint[0x1]) ACPI: LAPIC_NMI (acpi_id[0x01] high edge lint[0x1]) ACPI: LAPIC_NMI (acpi_id[0x02] high edge lint[0x1]) ACPI: LAPIC_NMI (acpi_id[0x03] high edge lint[0x1]) ACPI: IOAPIC (id[0x02] address[0xfec00000] gsi_base[0]) IOAPIC[0]: apic_id 2, version 32, address 0xfec00000, GSI 0-23 ACPI: IOAPIC (id[0x03] address[0xfec80000] gsi_base[24]) IOAPIC[1]: apic_id 3, version 32, address 0xfec80000, GSI 24-47 ACPI: IOAPIC (id[0x04] address[0xfec80400] gsi_base[48]) IOAPIC[2]: apic_id 4, version 32, address 0xfec80400, GSI 48-71 ACPI: INT_SRC_OVR (bus 0 bus_irq 0 global_irq 2 high edge) ACPI: INT_SRC_OVR (bus 0 bus_irq 9 global_irq 9 high level) ACPI: IRQ0 used by override. ACPI: IRQ2 used by override. ACPI: IRQ9 used by override. Enabling APIC mode: Flat. Using 3 I/O APICs Using ACPI (MADT) for SMP configuration information Allocating PCI resources starting at 50000000 (gap: 40000000:bec00000) Detected 2392.198 MHz processor. Built 1 zonelists. Total pages: 262000 Kernel command line: ro root=/dev/VolGroup00/LogVol00 rhgb mapped APIC to ffffd000 (fee00000) mapped IOAPIC to ffffc000 (fec00000) mapped IOAPIC to ffffb000 (fec80000) mapped IOAPIC to ffffa000 (fec80400) Enabling fast FPU save and restore... done. Enabling unmasked SIMD FPU exception support... done. Initializing CPU#0 CPU 0 irqstacks, hard=c0755000 soft=c0735000 PID hash table entries: 4096 (order: 12, 16384 bytes) Console: colour VGA+ 80x25 Dentry cache hash table entries: 131072 (order: 7, 524288 bytes) Inode-cache hash table entries: 65536 (order: 6, 262144 bytes) Memory: 1030992k/1048000k available (2124k kernel code, 16344k reserved, 885k data, 228k init, 130496k highmem) Checking if this processor honours the WP bit even in supervisor mode... Ok. Calibrating delay using timer specific routine.. 4786.48 BogoMIPS (lpj=2393244) Security Framework v1.0.0 initialized SELinux: Initializing. SELinux: Starting in permissive mode selinux_register_security: Registering secondary module capability Capability LSM initialized as secondary Mount-cache hash table entries: 512 CPU: After generic identify, caps: bfebfbff 00000000 00000000 00000000 00004400 00000000 00000000 CPU: After vendor identify, caps: bfebfbff 00000000 00000000 00000000 00004400 00000000 00000000 CPU: Trace cache: 12K uops, L1 D cache: 8K CPU: L2 cache: 512K CPU: Physical Processor ID: 0 CPU: After all inits, caps: bfebf3ff 00000000 00000000 00000080 00004400 00000000 00000000 Intel machine check architecture supported. Intel machine check reporting enabled on CPU#0. CPU0: Intel P4/Xeon Extended MCE MSRs (12) available CPU0: Thermal monitoring enabled Checking 'hlt' instruction... OK. SMP alternatives: switching to UP code ACPI: Core revision 20060707 CPU0: Intel(R) Xeon(TM) CPU 2.40GHz stepping 05 SMP alternatives: switching to SMP code Booting processor 1/1 eip 3000 CPU 1 irqstacks, hard=c0756000 soft=c0736000 Initializing CPU#1 Calibrating delay using timer specific routine.. 4783.40 BogoMIPS (lpj=2391702) CPU: After generic identify, caps: bfebfbff 00000000 00000000 00000000 00004400 00000000 00000000 CPU: After vendor identify, caps: bfebfbff 00000000 00000000 00000000 00004400 00000000 00000000 CPU: Trace cache: 12K uops, L1 D cache: 8K CPU: L2 cache: 512K CPU: Physical Processor ID: 0 CPU: After all inits, caps: bfebf3ff 00000000 00000000 00000080 00004400 00000000 00000000 Intel machine check architecture supported. Intel machine check reporting enabled on CPU#1. CPU1: Intel P4/Xeon Extended MCE MSRs (12) available CPU1: Thermal monitoring enabled CPU1: Intel(R) Xeon(TM) CPU 2.40GHz stepping 05 SMP alternatives: switching to SMP code Booting processor 2/6 eip 3000 CPU 2 irqstacks, hard=c0757000 soft=c0737000 Initializing CPU#2 Calibrating delay using timer specific routine.. 4783.44 BogoMIPS (lpj=2391723) CPU: After generic identify, caps: bfebfbff 00000000 00000000 00000000 00004400 00000000 00000000 CPU: After vendor identify, caps: bfebfbff 00000000 00000000 00000000 00004400 00000000 00000000 CPU: Trace cache: 12K uops, L1 D cache: 8K CPU: L2 cache: 512K CPU: Physical Processor ID: 3 CPU: After all inits, caps: bfebf3ff 00000000 00000000 00000080 00004400 00000000 00000000 Intel machine check architecture supported. Intel machine check reporting enabled on CPU#2. CPU2: Intel P4/Xeon Extended MCE MSRs (12) available CPU2: Thermal monitoring enabled CPU2: Intel(R) Xeon(TM) CPU 2.40GHz stepping 05 SMP alternatives: switching to SMP code Booting processor 3/7 eip 3000 CPU 3 irqstacks, hard=c0758000 soft=c0738000 Initializing CPU#3 Calibrating delay using timer specific routine.. 4783.42 BogoMIPS (lpj=2391714) CPU: After generic identify, caps: bfebfbff 00000000 00000000 00000000 00004400 00000000 00000000 CPU: After vendor identify, caps: bfebfbff 00000000 00000000 00000000 00004400 00000000 00000000 CPU: Trace cache: 12K uops, L1 D cache: 8K CPU: L2 cache: 512K CPU: Physical Processor ID: 3 CPU: After all inits, caps: bfebf3ff 00000000 00000000 00000080 00004400 00000000 00000000 Intel machine check architecture supported. Intel machine check reporting enabled on CPU#3. CPU3: Intel P4/Xeon Extended MCE MSRs (12) available CPU3: Thermal monitoring enabled CPU3: Intel(R) Xeon(TM) CPU 2.40GHz stepping 05 Total of 4 processors activated (19136.76 BogoMIPS). ENABLING IO-APIC IRQs ..TIMER: vector=0x31 apic1=0 pin1=2 apic2=-1 pin2=-1 checking TSC synchronization across 4 CPUs: passed. Brought up 4 CPUs sizeof(vma)=84 bytes sizeof(page)=32 bytes sizeof(inode)=340 bytes sizeof(dentry)=136 bytes sizeof(ext3inode)=492 bytes sizeof(buffer_head)=52 bytes sizeof(skbuff)=172 bytes migration_cost=61,655 checking if image is initramfs... it is Freeing initrd memory: 3130k freed NET: Registered protocol family 16 No dock devices found. ACPI: bus type pci registered PCI: PCI BIOS revision 2.10 entry at 0xfd8f5, last bus=5 PCI: Using configuration type 1 Setting up standard PCI resources ACPI: Interpreter enabled ACPI: Using IOAPIC for interrupt routing ACPI: PCI Root Bridge [PCI0] (0000:00) * The chipset may have PM-Timer Bug. Due to workarounds for a bug, * this clock source is slow. If you are sure your timer does not have * this bug, please use "acpi_pm_good" to disable the workaround PCI quirk: region 1000-107f claimed by ICH4 ACPI/GPIO/TCO PCI quirk: region 1180-11bf claimed by ICH4 GPIO PCI: Ignoring BAR0-3 of IDE controller 0000:00:1f.1 Boot video device is 0000:01:00.0 PCI: Firmware left 0000:05:03.0 e100 interrupts enabled, disabling PCI: Transparent bridge - 0000:00:1e.0 ACPI: PCI Interrupt Routing Table [_SB_.PCI0._PRT] ACPI: PCI Interrupt Link [LNKA] (IRQs 3 4 5 7 10 *11 14 15) ACPI: PCI Interrupt Link [LNKB] (IRQs 3 4 5 7 10 11 14 15) *0, disabled. ACPI: PCI Interrupt Link [LNKC] (IRQs 3 4 *5 7 10 11 14 15) ACPI: PCI Interrupt Link [LNKD] (IRQs 3 4 5 7 *10 11 14 15) ACPI: PCI Interrupt Link [LNKE] (IRQs 3 4 5 7 10 *11 14 15) ACPI: PCI Interrupt Link [LNKF] (IRQs 3 4 5 7 10 11 14 15) *0, disabled. ACPI: PCI Interrupt Link [LNKG] (IRQs 3 4 5 7 10 *11 14 15) ACPI: PCI Interrupt Link [LNKH] (IRQs 3 4 5 7 10 *11 14 15) ACPI: PCI Interrupt Routing Table [_SB_.PCI0.ICH4._PRT] ACPI: PCI Interrupt Routing Table [_SB_.PCI0.HLB_.Z000._PRT] ACPI: PCI Interrupt Routing Table [_SB_.PCI0.HLB_.Z001._PRT] ACPI: PCI Interrupt Routing Table [_SB_.PCI0.AGP_._PRT] Linux Plug and Play Support v0.97 (c) Adam Belay pnp: PnP ACPI init pnp: PnP ACPI: found 13 devices usbcore: registered new driver usbfs usbcore: registered new driver hub PCI: Using ACPI for IRQ routing PCI: If a device doesn't work, try "pci=routeirq". If it helps, post a report NetLabel: Initializing NetLabel: domain hash size = 128 NetLabel: protocols = UNLABELED CIPSOv4 NetLabel: unlabeled traffic allowed by default PCI: mem resource #6:20000@f8000000 for 0000:01:00.0 was not allocated. PCI: Bridge: 0000:00:01.0 IO window: disabled. MEM window: d1000000-d1ffffff PREFETCH window: f0000000-f7ffffff PCI: Bridge: 0000:02:1d.0 IO window: disabled. MEM window: disabled. PREFETCH window: disabled. PCI: Bridge: 0000:02:1f.0 IO window: 7000-7fff MEM window: d2100000-d21fffff PREFETCH window: disabled. PCI: Bridge: 0000:00:02.0 IO window: 7000-7fff MEM window: d2000000-d21fffff PREFETCH window: disabled. PCI: Bridge: 0000:00:1e.0 IO window: 8000-8fff MEM window: d2200000-d22fffff PREFETCH window: disabled. PCI: Setting latency timer of device 0000:00:1e.0 to 64 NET: Registered protocol family 2 IP route cache hash table entries: 32768 (order: 5, 131072 bytes) TCP established hash table entries: 131072 (order: 8, 1048576 bytes) TCP bind hash table entries: 65536 (order: 7, 524288 bytes) TCP: Hash tables configured (established 131072 bind 65536) TCP reno registered Simple Boot Flag at 0x35 set to 0x80 apm: BIOS not found. audit: initializing netlink socket (disabled) type=2000 audit(1249916375.100:1): initialized highmem bounce pool size: 64 pages Total HugeTLB memory allocated, 0 VFS: Disk quotas dquot_6.5.1 Dquot-cache hash table entries: 1024 (order 0, 4096 bytes) SELinux: Registering netfilter hooks Initializing Cryptographic API alg: No test for crc32c (crc32c-generic) ksign: Installing public key data Loading keyring - Added public key E5930ADED89DE961 - User ID: CentOS (Kernel Module GPG key) io scheduler noop registered io scheduler anticipatory registered io scheduler deadline registered io scheduler cfq registered (default) pci_hotplug: PCI Hot Plug PCI Core version: 0.5 Real Time Clock Driver v1.12ac Non-volatile memory driver v1.2 Linux agpgart interface v0.101 (c) Dave Jones agpgart: Detected an Intel E7505 Chipset. agpgart: AGP aperture is 256M @ 0xe0000000 Serial: 8250/16550 driver $Revision: 1.90 $ 4 ports, IRQ sharing enabled serial8250: ttyS0 at I/O 0x3f8 (irq = 4) is a 16550A serial8250: ttyS1 at I/O 0x2f8 (irq = 3) is a 16550A 00:0a: ttyS0 at I/O 0x3f8 (irq = 4) is a 16550A 00:0b: ttyS1 at I/O 0x2f8 (irq = 3) is a 16550A RAMDISK driver initialized: 16 RAM disks of 16384K size 4096 blocksize Uniform Multi-Platform E-IDE driver Revision: 7.00alpha2 ide: Assuming 33MHz system bus speed for PIO modes; override with idebus=xx ICH4: IDE controller at PCI slot 0000:00:1f.1 PCI: Enabling device 0000:00:1f.1 (0005 -> 0007) ACPI: PCI Interrupt 0000:00:1f.1[A] -> GSI 18 (level, low) -> IRQ 169 ICH4: chipset revision 2 ICH4: not 100% native mode: will probe irqs later ide0: BM-DMA at 0x6860-0x6867, BIOS settings: hda:DMA, hdb:DMA ide1: BM-DMA at 0x6868-0x686f, BIOS settings: hdc:DMA, hdd:DMA Probing IDE interface ide0... hda: WDC WD800JB-00ETA0, ATA DISK drive hdb: WDC WD10EADS-00L5B1, ATA DISK drive ide0 at 0x1f0-0x1f7,0x3f6 on irq 14 Probing IDE interface ide1... hdc: LITE-ON LTR-52327S, ATAPI CD/DVD-ROM drive hdd: IOMEGA ZIP 250 ATAPI, ATAPI FLOPPY drive ide1 at 0x170-0x177,0x376 on irq 15 hda: max request size: 512KiB hda: 156301488 sectors (80026 MB) w/8192KiB Cache, CHS=16383/255/63, UDMA(100) hda: cache flushes supported hda: hda1 hda2 hdb: max request size: 512KiB hdb: 1953525168 sectors (1000204 MB) w/32767KiB Cache, CHS=65535/255/63, UDMA(100) hdb: cache flushes supported hdb: hdb1 ide-floppy driver 0.99.newide hdd: No disk in drive hdd: 0kB, 0/64/32 CHS, 4096 kBps, 512 sector size, 2941 rpm usbcore: registered new driver hiddev usbcore: registered new driver usbhid drivers/usb/input/hid-core.c: v2.6:USB HID core driver PNP: PS/2 Controller [PNP0303:PS2K,PNP0f13:PS2M] at 0x60,0x64 irq 1,12 serio: i8042 KBD port at 0x60,0x64 irq 1 serio: i8042 AUX port at 0x60,0x64 irq 12 mice: PS/2 mouse device common for all mice md: md driver 0.90.3 MAX_MD_DEVS=256, MD_SB_DISKS=27 md: bitmap version 4.39 TCP bic registered Initializing IPsec netlink socket NET: Registered protocol family 1 NET: Registered protocol family 17 Using IPI No-Shortcut mode ACPI: (supports S0<6>Time: tsc clocksource has been installed. S1 S4 S5) Freeing unused kernel memory: 228k freed Write protecting the kernel read-only data: 397k ACPI: PCI Interrupt 0000:00:1d.7[D] -> GSI 23 (level, low) -> IRQ 177 PCI: Setting latency timer of device 0000:00:1d.7 to 64 ehci_hcd 0000:00:1d.7: EHCI Host Controller ehci_hcd 0000:00:1d.7: new USB bus registered, assigned bus number 1 ehci_hcd 0000:00:1d.7: debug port 1 PCI: cache line size of 128 is not supported by device 0000:00:1d.7 ehci_hcd 0000:00:1d.7: irq 177, io mem 0xd0000000 ehci_hcd 0000:00:1d.7: USB 2.0 started, EHCI 1.00, driver 10 Dec 2004 usb usb1: configuration #1 chosen from 1 choice hub 1-0:1.0: USB hub found hub 1-0:1.0: 6 ports detected ohci_hcd: 2005 April 22 USB 1.1 'Open' Host Controller (OHCI) Driver (PCI) USB Universal Host Controller Interface driver v3.0 ACPI: PCI Interrupt 0000:00:1d.0[A] -> GSI 16 (level, low) -> IRQ 185 PCI: Setting latency timer of device 0000:00:1d.0 to 64 uhci_hcd 0000:00:1d.0: UHCI Host Controller uhci_hcd 0000:00:1d.0: new USB bus registered, assigned bus number 2 uhci_hcd 0000:00:1d.0: irq 185, io base 0x00006800 usb usb2: configuration #1 chosen from 1 choice hub 2-0:1.0: USB hub found hub 2-0:1.0: 2 ports detected ACPI: PCI Interrupt 0000:00:1d.1[B] -> GSI 19 (level, low) -> IRQ 193 PCI: Setting latency timer of device 0000:00:1d.1 to 64 uhci_hcd 0000:00:1d.1: UHCI Host Controller uhci_hcd 0000:00:1d.1: new USB bus registered, assigned bus number 3 uhci_hcd 0000:00:1d.1: irq 193, io base 0x00006820 usb usb3: configuration #1 chosen from 1 choice hub 3-0:1.0: USB hub found hub 3-0:1.0: 2 ports detected ACPI: PCI Interrupt 0000:00:1d.2[C] -> GSI 18 (level, low) -> IRQ 169 PCI: Setting latency timer of device 0000:00:1d.2 to 64 uhci_hcd 0000:00:1d.2: UHCI Host Controller uhci_hcd 0000:00:1d.2: new USB bus registered, assigned bus number 4 uhci_hcd 0000:00:1d.2: irq 169, io base 0x00006840 usb usb4: configuration #1 chosen from 1 choice hub 4-0:1.0: USB hub found hub 4-0:1.0: 2 ports detected hdd: No disk in drive usb 2-1: new low speed USB device using uhci_hcd and address 2 usb 2-1: configuration #1 chosen from 1 choice input: Rextron USB as /class/input/input0 input: USB HID v1.00 Keyboard [Rextron USB] on usb-0000:00:1d.0-1 input: Rextron USB as /class/input/input1 input: USB HID v1.10 Mouse [Rextron USB] on usb-0000:00:1d.0-1 SCSI subsystem initialized libata version 3.00 loaded. device-mapper: uevent: version 1.0.3 device-mapper: ioctl: 4.11.5-ioctl (2007-12-12) initialised: dm-devel@redhat.com device-mapper: dm-raid45: initialized v0.2429 hdd: No disk in drive hdd: No disk in drive hdd: No disk in drive hdd: No disk in drive kjournald starting. Commit interval 5 seconds EXT3-fs: mounted filesystem with ordered data mode. security: 3 users, 6 roles, 1914 types, 234 bools, 1 sens, 1024 cats security: 61 classes, 69080 rules SELinux: Completing initialization. SELinux: Setting up existing superblocks. SELinux: initialized (dev dm-0, type ext3), uses xattr SELinux: initialized (dev usbfs, type usbfs), uses genfs_contexts SELinux: initialized (dev tmpfs, type tmpfs), uses transition SIDs SELinux: initialized (dev debugfs, type debugfs), uses genfs_contexts SELinux: initialized (dev selinuxfs, type selinuxfs), uses genfs_contexts SELinux: initialized (dev mqueue, type mqueue), uses transition SIDs SELinux: initialized (dev hugetlbfs, type hugetlbfs), uses genfs_contexts SELinux: initialized (dev devpts, type devpts), uses transition SIDs SELinux: initialized (dev eventpollfs, type eventpollfs), uses task SIDs SELinux: initialized (dev inotifyfs, type inotifyfs), uses genfs_contexts SELinux: initialized (dev tmpfs, type tmpfs), uses transition SIDs SELinux: initialized (dev futexfs, type futexfs), uses genfs_contexts SELinux: initialized (dev anon_inodefs, type anon_inodefs), uses genfs_contexts SELinux: initialized (dev pipefs, type pipefs), uses task SIDs SELinux: initialized (dev sockfs, type sockfs), uses task SIDs SELinux: initialized (dev cpuset, type cpuset), uses genfs_contexts SELinux: initialized (dev proc, type proc), uses genfs_contexts SELinux: initialized (dev bdev, type bdev), uses genfs_contexts SELinux: initialized (dev rootfs, type rootfs), uses genfs_contexts SELinux: initialized (dev sysfs, type sysfs), uses genfs_contexts type=1403 audit(1249916400.115:2): policy loaded auid=4294967295 ses=4294967295 e100: Intel(R) PRO/100 Network Driver, 3.5.10-k2-NAPI e100: Copyright(c) 1999-2005 Intel Corporation ACPI: PCI Interrupt 0000:05:03.0[A] -> GSI 18 (level, low) -> IRQ 169 e100: eth0: e100_probe: addr 0xd2220000, irq 169, MAC addr 00:04:23:88:86:55 Intel(R) PRO/1000 Network Driver - version 7.3.20-k2-NAPI Copyright (c) 1999-2006 Intel Corporation. ACPI: PCI Interrupt 0000:04:02.0[A] -> GSI 52 (level, low) -> IRQ 201 e1000: 0000:04:02.0: e1000_probe: (PCI:66MHz:32-bit) 00:04:23:88:87:43 e1000: eth1: e1000_probe: Intel(R) PRO/1000 Network Connection hdc: ATAPI 52X CD-ROM CD-R/RW drive, 2048kB Cache, UDMA(33) Uniform CD-ROM driver Revision: 3.20 gameport: EMU10K1 is pci0000:05:01.1/gameport0, io 0x8060, speed 962kHz parport: PnPBIOS parport detected. parport0: PC-style at 0x378 (0x778), irq 7 [PCSPP,TRISTATE,EPP] ACPI: PCI Interrupt 0000:00:1f.3[B] -> GSI 17 (level, low) -> IRQ 209 input: PC Speaker as /class/input/input2 Floppy drive(s): fd0 is 1.44M EDAC MC: Ver: 2.0.1 Jun 17 2009 FDC 0 is a post-1991 82077 ACPI: PCI Interrupt 0000:05:01.0[A] -> GSI 22 (level, low) -> IRQ 217 lp0: using parport0 (interrupt-driven). lp0: console ready SELinux: initialized (dev ramfs, type ramfs), uses genfs_contexts NET: Registered protocol family 10 lo: Disabled Privacy Extensions IPv6 over IPv4 tunneling driver ACPI: Power Button (FF) [PWRF] ACPI: Power Button (CM) [PWRB] md: Autodetecting RAID arrays. md: autorun ... md: ... autorun DONE. device-mapper: multipath: version 1.0.5 loaded EXT3 FS on dm-0, internal journal kjournald starting. Commit interval 5 seconds EXT3 FS on dm-1, internal journal EXT3-fs: mounted filesystem with ordered data mode. SELinux: initialized (dev dm-1, type ext3), uses xattr kjournald starting. Commit interval 5 seconds EXT3 FS on hda1, internal journal EXT3-fs: mounted filesystem with ordered data mode. SELinux: initialized (dev hda1, type ext3), uses xattr SELinux: initialized (dev tmpfs, type tmpfs), uses transition SIDs Adding 2031608k swap on /dev/VolGroup00/LogVol02. Priority:-1 extents:1 across:2031608k SELinux: initialized (dev binfmt_misc, type binfmt_misc), uses genfs_contexts IA-32 Microcode Update Driver: v1.14a tigran@veritas.com microcode: CPU2 updated from revision 0x14 to 0x29, date = 08112004 microcode: CPU1 updated from revision 0x14 to 0x29, date = 08112004 microcode: CPU3 updated from revision 0x14 to 0x29, date = 08112004 microcode: CPU0 updated from revision 0x14 to 0x29, date = 08112004 ip6_tables: (C) 2000-2006 Netfilter Core Team ip_tables: (C) 2000-2006 Netfilter Core Team Netfilter messages via NETLINK v0.30. ip_conntrack version 2.4 (8187 buckets, 65496 max) - 228 bytes per conntrack ADDRCONF(NETDEV_UP): eth0: link is not ready e100: eth0: e100_watchdog: link up, 100Mbps, full-duplex ADDRCONF(NETDEV_CHANGE): eth0: link becomes ready libafs: module license 'http://www.openafs.org/dl/license10.html' taints kernel. Found system call table at 0xc06154e0 (pattern scan) Address 0xc06154e0 is not writable. System call hooks will not be installed; proceeding anyway enabling dynamically allocated vcaches Starting AFS cache scan...found 677 non-empty cache files (8%). SELinux: initialized (dev afs, type afs), uses genfs_contexts eth0: no IPv6 routers present SELinux: initialized (dev rpc_pipefs, type rpc_pipefs), uses genfs_contexts Bluetooth: Core ver 2.10 NET: Registered protocol family 31 Bluetooth: HCI device and connection manager initialized Bluetooth: HCI socket layer initialized Bluetooth: L2CAP ver 2.8 Bluetooth: L2CAP socket layer initialized Bluetooth: RFCOMM socket layer initialized Bluetooth: RFCOMM TTY layer initialized Bluetooth: RFCOMM ver 1.8 Bluetooth: HIDP (Human Interface Emulation) ver 1.1 SELinux: initialized (dev autofs, type autofs), uses genfs_contexts SELinux: initialized (dev autofs, type autofs), uses genfs_contexts SELinux: initialized (dev autofs, type autofs), uses genfs_contexts hdd: No disk in drive
2009/8/10 Pedro Paulo de Magalhães Oliveira Junior ppj@netfilter.com.br
Can you post the output of dmesg command
Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br --- Em breve Netfilter Small Business
2009/8/10 corinna bauer corinnab83@gmail.com
That didn't work. Corinna
2009/8/10 Pedro Paulo de Magalhães Oliveira Junior ppj@netfilter.com.br
try:
setenv doublebufferflag 1
before running tksurfer
Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br --- Em breve Netfilter Small Business
2009/8/10 corinna bauer corinnab83@gmail.com
When I run tksurfer, only portions of the cuneus, lateral occipital, and superior parietal regions are displayed. This occurs in both FS versions 4.2.0 and 4.4.0. I am using a 32 bit BU Linux system which is equivalent to redhat 5.0. The error message is similar to those in previous posts, but previous suggestions don't seem to help.
surfer: current subjects dir: /home/freesurfer4.2.0/subjects/corinna/PET surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/freesurfer4.2.0/subjects/corinna/PET surfer: Reading header info from /home/freesurfer4.2.0/subjects/corinna/PET/003_S_1059/mri/T1.mgz surfer: vertices=119899, faces=239794 Loading /home/freesurfer4.2.0/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(003_S_1059) surfer: using interface /home/freesurfer4.2.0/lib/tcl/tksurfer.tcl Reading /home/freesurfer4.2.0/lib/tcl/tkm_common.tcl Reading /home/freesurfer4.2.0/lib/tcl/tkm_wrappers.tcl Reading /home/freesurfer4.2.0/lib/tcl/fsgdfPlot.tcl Reading /home/freesurfer4.2.0/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
what is the graphics card, and is the driver the most current available?
On Mon, 2009-08-10 at 17:28 -0400, corinna bauer wrote:
The output from dmesg is:
Linux version 2.6.18-128.1.14.el5 (mockbuild@builder16.centos.org) (gcc version 4.1.2 20080704 (Red Hat 4.1.2-44)) #1 SMP Wed Jun 17 06:40:54 EDT 2009 BIOS-provided physical RAM map: BIOS-e820: 0000000000000000 - 000000000009b800 (usable) BIOS-e820: 000000000009b800 - 00000000000a0000 (reserved) BIOS-e820: 00000000000e0000 - 0000000000100000 (reserved) BIOS-e820: 0000000000100000 - 000000003ff70000 (usable) BIOS-e820: 000000003ff70000 - 000000003ff7b000 (ACPI data) BIOS-e820: 000000003ff7b000 - 000000003ff80000 (ACPI NVS) BIOS-e820: 000000003ff80000 - 0000000040000000 (reserved) BIOS-e820: 00000000fec00000 - 00000000fec10000 (reserved) BIOS-e820: 00000000fee00000 - 00000000fee01000 (reserved) BIOS-e820: 00000000ff800000 - 00000000ffc00000 (reserved) BIOS-e820: 00000000fff00000 - 0000000100000000 (reserved) 127MB HIGHMEM available. 896MB LOWMEM available. found SMP MP-table at 000f6120 Memory for crash kernel (0x0 to 0x0) notwithin permissible range disabling kdump Using x86 segment limits to approximate NX protection On node 0 totalpages: 262000 DMA zone: 4096 pages, LIFO batch:0 Normal zone: 225280 pages, LIFO batch:31 HighMem zone: 32624 pages, LIFO batch:7 DMI present. Using APIC driver default ACPI: RSDP (v000 PTLTD ) @ 0x000f6160 ACPI: RSDT (v001 PTLTD RSDT 0x06040000 LTP 0x00000000) @ 0x3ff76ee4 ACPI: FADT (v001 INTEL E7505 0x06040000 PTL 0x00000008) @ 0x3ff7ae78 ACPI: MADT (v001 PTLTD APIC 0x06040000 LTP 0x00000000) @ 0x3ff7aeec ACPI: BOOT (v001 PTLTD $SBFTBL$ 0x06040000 LTP 0x00000001) @ 0x3ff7af88 ACPI: SPCR (v001 PTLTD $UCRTBL$ 0x06040000 PTL 0x00000001) @ 0x3ff7afb0 ACPI: DSDT (v001 INTEL E7505 0x06040000 MSFT 0x0100000e) @ 0x00000000 ACPI: PM-Timer IO Port: 0x1008 ACPI: Local APIC address 0xfee00000 ACPI: LAPIC (acpi_id[0x00] lapic_id[0x00] enabled) Processor #0 15:2 APIC version 20 ACPI: LAPIC (acpi_id[0x01] lapic_id[0x06] enabled) Processor #6 15:2 APIC version 20 ACPI: LAPIC (acpi_id[0x02] lapic_id[0x01] enabled) Processor #1 15:2 APIC version 20 ACPI: LAPIC (acpi_id[0x03] lapic_id[0x07] enabled) Processor #7 15:2 APIC version 20 ACPI: LAPIC_NMI (acpi_id[0x00] high edge lint[0x1]) ACPI: LAPIC_NMI (acpi_id[0x01] high edge lint[0x1]) ACPI: LAPIC_NMI (acpi_id[0x02] high edge lint[0x1]) ACPI: LAPIC_NMI (acpi_id[0x03] high edge lint[0x1]) ACPI: IOAPIC (id[0x02] address[0xfec00000] gsi_base[0]) IOAPIC[0]: apic_id 2, version 32, address 0xfec00000, GSI 0-23 ACPI: IOAPIC (id[0x03] address[0xfec80000] gsi_base[24]) IOAPIC[1]: apic_id 3, version 32, address 0xfec80000, GSI 24-47 ACPI: IOAPIC (id[0x04] address[0xfec80400] gsi_base[48]) IOAPIC[2]: apic_id 4, version 32, address 0xfec80400, GSI 48-71 ACPI: INT_SRC_OVR (bus 0 bus_irq 0 global_irq 2 high edge) ACPI: INT_SRC_OVR (bus 0 bus_irq 9 global_irq 9 high level) ACPI: IRQ0 used by override. ACPI: IRQ2 used by override. ACPI: IRQ9 used by override. Enabling APIC mode: Flat. Using 3 I/O APICs Using ACPI (MADT) for SMP configuration information Allocating PCI resources starting at 50000000 (gap: 40000000:bec00000) Detected 2392.198 MHz processor. Built 1 zonelists. Total pages: 262000 Kernel command line: ro root=/dev/VolGroup00/LogVol00 rhgb mapped APIC to ffffd000 (fee00000) mapped IOAPIC to ffffc000 (fec00000) mapped IOAPIC to ffffb000 (fec80000) mapped IOAPIC to ffffa000 (fec80400) Enabling fast FPU save and restore... done. Enabling unmasked SIMD FPU exception support... done. Initializing CPU#0 CPU 0 irqstacks, hard=c0755000 soft=c0735000 PID hash table entries: 4096 (order: 12, 16384 bytes) Console: colour VGA+ 80x25 Dentry cache hash table entries: 131072 (order: 7, 524288 bytes) Inode-cache hash table entries: 65536 (order: 6, 262144 bytes) Memory: 1030992k/1048000k available (2124k kernel code, 16344k reserved, 885k data, 228k init, 130496k highmem) Checking if this processor honours the WP bit even in supervisor mode... Ok. Calibrating delay using timer specific routine.. 4786.48 BogoMIPS (lpj=2393244) Security Framework v1.0.0 initialized SELinux: Initializing. SELinux: Starting in permissive mode selinux_register_security: Registering secondary module capability Capability LSM initialized as secondary Mount-cache hash table entries: 512 CPU: After generic identify, caps: bfebfbff 00000000 00000000 00000000 00004400 00000000 00000000 CPU: After vendor identify, caps: bfebfbff 00000000 00000000 00000000 00004400 00000000 00000000 CPU: Trace cache: 12K uops, L1 D cache: 8K CPU: L2 cache: 512K CPU: Physical Processor ID: 0 CPU: After all inits, caps: bfebf3ff 00000000 00000000 00000080 00004400 00000000 00000000 Intel machine check architecture supported. Intel machine check reporting enabled on CPU#0. CPU0: Intel P4/Xeon Extended MCE MSRs (12) available CPU0: Thermal monitoring enabled Checking 'hlt' instruction... OK. SMP alternatives: switching to UP code ACPI: Core revision 20060707 CPU0: Intel(R) Xeon(TM) CPU 2.40GHz stepping 05 SMP alternatives: switching to SMP code Booting processor 1/1 eip 3000 CPU 1 irqstacks, hard=c0756000 soft=c0736000 Initializing CPU#1 Calibrating delay using timer specific routine.. 4783.40 BogoMIPS (lpj=2391702) CPU: After generic identify, caps: bfebfbff 00000000 00000000 00000000 00004400 00000000 00000000 CPU: After vendor identify, caps: bfebfbff 00000000 00000000 00000000 00004400 00000000 00000000 CPU: Trace cache: 12K uops, L1 D cache: 8K CPU: L2 cache: 512K CPU: Physical Processor ID: 0 CPU: After all inits, caps: bfebf3ff 00000000 00000000 00000080 00004400 00000000 00000000 Intel machine check architecture supported. Intel machine check reporting enabled on CPU#1. CPU1: Intel P4/Xeon Extended MCE MSRs (12) available CPU1: Thermal monitoring enabled CPU1: Intel(R) Xeon(TM) CPU 2.40GHz stepping 05 SMP alternatives: switching to SMP code Booting processor 2/6 eip 3000 CPU 2 irqstacks, hard=c0757000 soft=c0737000 Initializing CPU#2 Calibrating delay using timer specific routine.. 4783.44 BogoMIPS (lpj=2391723) CPU: After generic identify, caps: bfebfbff 00000000 00000000 00000000 00004400 00000000 00000000 CPU: After vendor identify, caps: bfebfbff 00000000 00000000 00000000 00004400 00000000 00000000 CPU: Trace cache: 12K uops, L1 D cache: 8K CPU: L2 cache: 512K CPU: Physical Processor ID: 3 CPU: After all inits, caps: bfebf3ff 00000000 00000000 00000080 00004400 00000000 00000000 Intel machine check architecture supported. Intel machine check reporting enabled on CPU#2. CPU2: Intel P4/Xeon Extended MCE MSRs (12) available CPU2: Thermal monitoring enabled CPU2: Intel(R) Xeon(TM) CPU 2.40GHz stepping 05 SMP alternatives: switching to SMP code Booting processor 3/7 eip 3000 CPU 3 irqstacks, hard=c0758000 soft=c0738000 Initializing CPU#3 Calibrating delay using timer specific routine.. 4783.42 BogoMIPS (lpj=2391714) CPU: After generic identify, caps: bfebfbff 00000000 00000000 00000000 00004400 00000000 00000000 CPU: After vendor identify, caps: bfebfbff 00000000 00000000 00000000 00004400 00000000 00000000 CPU: Trace cache: 12K uops, L1 D cache: 8K CPU: L2 cache: 512K CPU: Physical Processor ID: 3 CPU: After all inits, caps: bfebf3ff 00000000 00000000 00000080 00004400 00000000 00000000 Intel machine check architecture supported. Intel machine check reporting enabled on CPU#3. CPU3: Intel P4/Xeon Extended MCE MSRs (12) available CPU3: Thermal monitoring enabled CPU3: Intel(R) Xeon(TM) CPU 2.40GHz stepping 05 Total of 4 processors activated (19136.76 BogoMIPS). ENABLING IO-APIC IRQs ..TIMER: vector=0x31 apic1=0 pin1=2 apic2=-1 pin2=-1 checking TSC synchronization across 4 CPUs: passed. Brought up 4 CPUs sizeof(vma)=84 bytes sizeof(page)=32 bytes sizeof(inode)=340 bytes sizeof(dentry)=136 bytes sizeof(ext3inode)=492 bytes sizeof(buffer_head)=52 bytes sizeof(skbuff)=172 bytes migration_cost=61,655 checking if image is initramfs... it is Freeing initrd memory: 3130k freed NET: Registered protocol family 16 No dock devices found. ACPI: bus type pci registered PCI: PCI BIOS revision 2.10 entry at 0xfd8f5, last bus=5 PCI: Using configuration type 1 Setting up standard PCI resources ACPI: Interpreter enabled ACPI: Using IOAPIC for interrupt routing ACPI: PCI Root Bridge [PCI0] (0000:00)
- The chipset may have PM-Timer Bug. Due to workarounds for a bug,
- this clock source is slow. If you are sure your timer does not have
- this bug, please use "acpi_pm_good" to disable the workaround
PCI quirk: region 1000-107f claimed by ICH4 ACPI/GPIO/TCO PCI quirk: region 1180-11bf claimed by ICH4 GPIO PCI: Ignoring BAR0-3 of IDE controller 0000:00:1f.1 Boot video device is 0000:01:00.0 PCI: Firmware left 0000:05:03.0 e100 interrupts enabled, disabling PCI: Transparent bridge - 0000:00:1e.0 ACPI: PCI Interrupt Routing Table [_SB_.PCI0._PRT] ACPI: PCI Interrupt Link [LNKA] (IRQs 3 4 5 7 10 *11 14 15) ACPI: PCI Interrupt Link [LNKB] (IRQs 3 4 5 7 10 11 14 15) *0, disabled. ACPI: PCI Interrupt Link [LNKC] (IRQs 3 4 *5 7 10 11 14 15) ACPI: PCI Interrupt Link [LNKD] (IRQs 3 4 5 7 *10 11 14 15) ACPI: PCI Interrupt Link [LNKE] (IRQs 3 4 5 7 10 *11 14 15) ACPI: PCI Interrupt Link [LNKF] (IRQs 3 4 5 7 10 11 14 15) *0, disabled. ACPI: PCI Interrupt Link [LNKG] (IRQs 3 4 5 7 10 *11 14 15) ACPI: PCI Interrupt Link [LNKH] (IRQs 3 4 5 7 10 *11 14 15) ACPI: PCI Interrupt Routing Table [_SB_.PCI0.ICH4._PRT] ACPI: PCI Interrupt Routing Table [_SB_.PCI0.HLB_.Z000._PRT] ACPI: PCI Interrupt Routing Table [_SB_.PCI0.HLB_.Z001._PRT] ACPI: PCI Interrupt Routing Table [_SB_.PCI0.AGP_._PRT] Linux Plug and Play Support v0.97 (c) Adam Belay pnp: PnP ACPI init pnp: PnP ACPI: found 13 devices usbcore: registered new driver usbfs usbcore: registered new driver hub PCI: Using ACPI for IRQ routing PCI: If a device doesn't work, try "pci=routeirq". If it helps, post a report NetLabel: Initializing NetLabel: domain hash size = 128 NetLabel: protocols = UNLABELED CIPSOv4 NetLabel: unlabeled traffic allowed by default PCI: mem resource #6:20000@f8000000 for 0000:01:00.0 was not allocated. PCI: Bridge: 0000:00:01.0 IO window: disabled. MEM window: d1000000-d1ffffff PREFETCH window: f0000000-f7ffffff PCI: Bridge: 0000:02:1d.0 IO window: disabled. MEM window: disabled. PREFETCH window: disabled. PCI: Bridge: 0000:02:1f.0 IO window: 7000-7fff MEM window: d2100000-d21fffff PREFETCH window: disabled. PCI: Bridge: 0000:00:02.0 IO window: 7000-7fff MEM window: d2000000-d21fffff PREFETCH window: disabled. PCI: Bridge: 0000:00:1e.0 IO window: 8000-8fff MEM window: d2200000-d22fffff PREFETCH window: disabled. PCI: Setting latency timer of device 0000:00:1e.0 to 64 NET: Registered protocol family 2 IP route cache hash table entries: 32768 (order: 5, 131072 bytes) TCP established hash table entries: 131072 (order: 8, 1048576 bytes) TCP bind hash table entries: 65536 (order: 7, 524288 bytes) TCP: Hash tables configured (established 131072 bind 65536) TCP reno registered Simple Boot Flag at 0x35 set to 0x80 apm: BIOS not found. audit: initializing netlink socket (disabled) type=2000 audit(1249916375.100:1): initialized highmem bounce pool size: 64 pages Total HugeTLB memory allocated, 0 VFS: Disk quotas dquot_6.5.1 Dquot-cache hash table entries: 1024 (order 0, 4096 bytes) SELinux: Registering netfilter hooks Initializing Cryptographic API alg: No test for crc32c (crc32c-generic) ksign: Installing public key data Loading keyring
- Added public key E5930ADED89DE961
- User ID: CentOS (Kernel Module GPG key)
io scheduler noop registered io scheduler anticipatory registered io scheduler deadline registered io scheduler cfq registered (default) pci_hotplug: PCI Hot Plug PCI Core version: 0.5 Real Time Clock Driver v1.12ac Non-volatile memory driver v1.2 Linux agpgart interface v0.101 (c) Dave Jones agpgart: Detected an Intel E7505 Chipset. agpgart: AGP aperture is 256M @ 0xe0000000 Serial: 8250/16550 driver $Revision: 1.90 $ 4 ports, IRQ sharing enabled serial8250: ttyS0 at I/O 0x3f8 (irq = 4) is a 16550A serial8250: ttyS1 at I/O 0x2f8 (irq = 3) is a 16550A 00:0a: ttyS0 at I/O 0x3f8 (irq = 4) is a 16550A 00:0b: ttyS1 at I/O 0x2f8 (irq = 3) is a 16550A RAMDISK driver initialized: 16 RAM disks of 16384K size 4096 blocksize Uniform Multi-Platform E-IDE driver Revision: 7.00alpha2 ide: Assuming 33MHz system bus speed for PIO modes; override with idebus=xx ICH4: IDE controller at PCI slot 0000:00:1f.1 PCI: Enabling device 0000:00:1f.1 (0005 -> 0007) ACPI: PCI Interrupt 0000:00:1f.1[A] -> GSI 18 (level, low) -> IRQ 169 ICH4: chipset revision 2 ICH4: not 100% native mode: will probe irqs later ide0: BM-DMA at 0x6860-0x6867, BIOS settings: hda:DMA, hdb:DMA ide1: BM-DMA at 0x6868-0x686f, BIOS settings: hdc:DMA, hdd:DMA Probing IDE interface ide0... hda: WDC WD800JB-00ETA0, ATA DISK drive hdb: WDC WD10EADS-00L5B1, ATA DISK drive ide0 at 0x1f0-0x1f7,0x3f6 on irq 14 Probing IDE interface ide1... hdc: LITE-ON LTR-52327S, ATAPI CD/DVD-ROM drive hdd: IOMEGA ZIP 250 ATAPI, ATAPI FLOPPY drive ide1 at 0x170-0x177,0x376 on irq 15 hda: max request size: 512KiB hda: 156301488 sectors (80026 MB) w/8192KiB Cache, CHS=16383/255/63, UDMA(100) hda: cache flushes supported hda: hda1 hda2 hdb: max request size: 512KiB hdb: 1953525168 sectors (1000204 MB) w/32767KiB Cache, CHS=65535/255/63, UDMA(100) hdb: cache flushes supported hdb: hdb1 ide-floppy driver 0.99.newide hdd: No disk in drive hdd: 0kB, 0/64/32 CHS, 4096 kBps, 512 sector size, 2941 rpm usbcore: registered new driver hiddev usbcore: registered new driver usbhid drivers/usb/input/hid-core.c: v2.6:USB HID core driver PNP: PS/2 Controller [PNP0303:PS2K,PNP0f13:PS2M] at 0x60,0x64 irq 1,12 serio: i8042 KBD port at 0x60,0x64 irq 1 serio: i8042 AUX port at 0x60,0x64 irq 12 mice: PS/2 mouse device common for all mice md: md driver 0.90.3 MAX_MD_DEVS=256, MD_SB_DISKS=27 md: bitmap version 4.39 TCP bic registered Initializing IPsec netlink socket NET: Registered protocol family 1 NET: Registered protocol family 17 Using IPI No-Shortcut mode ACPI: (supports S0<6>Time: tsc clocksource has been installed. S1 S4 S5) Freeing unused kernel memory: 228k freed Write protecting the kernel read-only data: 397k ACPI: PCI Interrupt 0000:00:1d.7[D] -> GSI 23 (level, low) -> IRQ 177 PCI: Setting latency timer of device 0000:00:1d.7 to 64 ehci_hcd 0000:00:1d.7: EHCI Host Controller ehci_hcd 0000:00:1d.7: new USB bus registered, assigned bus number 1 ehci_hcd 0000:00:1d.7: debug port 1 PCI: cache line size of 128 is not supported by device 0000:00:1d.7 ehci_hcd 0000:00:1d.7: irq 177, io mem 0xd0000000 ehci_hcd 0000:00:1d.7: USB 2.0 started, EHCI 1.00, driver 10 Dec 2004 usb usb1: configuration #1 chosen from 1 choice hub 1-0:1.0: USB hub found hub 1-0:1.0: 6 ports detected ohci_hcd: 2005 April 22 USB 1.1 'Open' Host Controller (OHCI) Driver (PCI) USB Universal Host Controller Interface driver v3.0 ACPI: PCI Interrupt 0000:00:1d.0[A] -> GSI 16 (level, low) -> IRQ 185 PCI: Setting latency timer of device 0000:00:1d.0 to 64 uhci_hcd 0000:00:1d.0: UHCI Host Controller uhci_hcd 0000:00:1d.0: new USB bus registered, assigned bus number 2 uhci_hcd 0000:00:1d.0: irq 185, io base 0x00006800 usb usb2: configuration #1 chosen from 1 choice hub 2-0:1.0: USB hub found hub 2-0:1.0: 2 ports detected ACPI: PCI Interrupt 0000:00:1d.1[B] -> GSI 19 (level, low) -> IRQ 193 PCI: Setting latency timer of device 0000:00:1d.1 to 64 uhci_hcd 0000:00:1d.1: UHCI Host Controller uhci_hcd 0000:00:1d.1: new USB bus registered, assigned bus number 3 uhci_hcd 0000:00:1d.1: irq 193, io base 0x00006820 usb usb3: configuration #1 chosen from 1 choice hub 3-0:1.0: USB hub found hub 3-0:1.0: 2 ports detected ACPI: PCI Interrupt 0000:00:1d.2[C] -> GSI 18 (level, low) -> IRQ 169 PCI: Setting latency timer of device 0000:00:1d.2 to 64 uhci_hcd 0000:00:1d.2: UHCI Host Controller uhci_hcd 0000:00:1d.2: new USB bus registered, assigned bus number 4 uhci_hcd 0000:00:1d.2: irq 169, io base 0x00006840 usb usb4: configuration #1 chosen from 1 choice hub 4-0:1.0: USB hub found hub 4-0:1.0: 2 ports detected hdd: No disk in drive usb 2-1: new low speed USB device using uhci_hcd and address 2 usb 2-1: configuration #1 chosen from 1 choice input: Rextron USB as /class/input/input0 input: USB HID v1.00 Keyboard [Rextron USB] on usb-0000:00:1d.0-1 input: Rextron USB as /class/input/input1 input: USB HID v1.10 Mouse [Rextron USB] on usb-0000:00:1d.0-1 SCSI subsystem initialized libata version 3.00 loaded. device-mapper: uevent: version 1.0.3 device-mapper: ioctl: 4.11.5-ioctl (2007-12-12) initialised: dm-devel@redhat.com device-mapper: dm-raid45: initialized v0.2429 hdd: No disk in drive hdd: No disk in drive hdd: No disk in drive hdd: No disk in drive kjournald starting. Commit interval 5 seconds EXT3-fs: mounted filesystem with ordered data mode. security: 3 users, 6 roles, 1914 types, 234 bools, 1 sens, 1024 cats security: 61 classes, 69080 rules SELinux: Completing initialization. SELinux: Setting up existing superblocks. SELinux: initialized (dev dm-0, type ext3), uses xattr SELinux: initialized (dev usbfs, type usbfs), uses genfs_contexts SELinux: initialized (dev tmpfs, type tmpfs), uses transition SIDs SELinux: initialized (dev debugfs, type debugfs), uses genfs_contexts SELinux: initialized (dev selinuxfs, type selinuxfs), uses genfs_contexts SELinux: initialized (dev mqueue, type mqueue), uses transition SIDs SELinux: initialized (dev hugetlbfs, type hugetlbfs), uses genfs_contexts SELinux: initialized (dev devpts, type devpts), uses transition SIDs SELinux: initialized (dev eventpollfs, type eventpollfs), uses task SIDs SELinux: initialized (dev inotifyfs, type inotifyfs), uses genfs_contexts SELinux: initialized (dev tmpfs, type tmpfs), uses transition SIDs SELinux: initialized (dev futexfs, type futexfs), uses genfs_contexts SELinux: initialized (dev anon_inodefs, type anon_inodefs), uses genfs_contexts SELinux: initialized (dev pipefs, type pipefs), uses task SIDs SELinux: initialized (dev sockfs, type sockfs), uses task SIDs SELinux: initialized (dev cpuset, type cpuset), uses genfs_contexts SELinux: initialized (dev proc, type proc), uses genfs_contexts SELinux: initialized (dev bdev, type bdev), uses genfs_contexts SELinux: initialized (dev rootfs, type rootfs), uses genfs_contexts SELinux: initialized (dev sysfs, type sysfs), uses genfs_contexts type=1403 audit(1249916400.115:2): policy loaded auid=4294967295 ses=4294967295 e100: Intel(R) PRO/100 Network Driver, 3.5.10-k2-NAPI e100: Copyright(c) 1999-2005 Intel Corporation ACPI: PCI Interrupt 0000:05:03.0[A] -> GSI 18 (level, low) -> IRQ 169 e100: eth0: e100_probe: addr 0xd2220000, irq 169, MAC addr 00:04:23:88:86:55 Intel(R) PRO/1000 Network Driver - version 7.3.20-k2-NAPI Copyright (c) 1999-2006 Intel Corporation. ACPI: PCI Interrupt 0000:04:02.0[A] -> GSI 52 (level, low) -> IRQ 201 e1000: 0000:04:02.0: e1000_probe: (PCI:66MHz:32-bit) 00:04:23:88:87:43 e1000: eth1: e1000_probe: Intel(R) PRO/1000 Network Connection hdc: ATAPI 52X CD-ROM CD-R/RW drive, 2048kB Cache, UDMA(33) Uniform CD-ROM driver Revision: 3.20 gameport: EMU10K1 is pci0000:05:01.1/gameport0, io 0x8060, speed 962kHz parport: PnPBIOS parport detected. parport0: PC-style at 0x378 (0x778), irq 7 [PCSPP,TRISTATE,EPP] ACPI: PCI Interrupt 0000:00:1f.3[B] -> GSI 17 (level, low) -> IRQ 209 input: PC Speaker as /class/input/input2 Floppy drive(s): fd0 is 1.44M EDAC MC: Ver: 2.0.1 Jun 17 2009 FDC 0 is a post-1991 82077 ACPI: PCI Interrupt 0000:05:01.0[A] -> GSI 22 (level, low) -> IRQ 217 lp0: using parport0 (interrupt-driven). lp0: console ready SELinux: initialized (dev ramfs, type ramfs), uses genfs_contexts NET: Registered protocol family 10 lo: Disabled Privacy Extensions IPv6 over IPv4 tunneling driver ACPI: Power Button (FF) [PWRF] ACPI: Power Button (CM) [PWRB] md: Autodetecting RAID arrays. md: autorun ... md: ... autorun DONE. device-mapper: multipath: version 1.0.5 loaded EXT3 FS on dm-0, internal journal kjournald starting. Commit interval 5 seconds EXT3 FS on dm-1, internal journal EXT3-fs: mounted filesystem with ordered data mode. SELinux: initialized (dev dm-1, type ext3), uses xattr kjournald starting. Commit interval 5 seconds EXT3 FS on hda1, internal journal EXT3-fs: mounted filesystem with ordered data mode. SELinux: initialized (dev hda1, type ext3), uses xattr SELinux: initialized (dev tmpfs, type tmpfs), uses transition SIDs Adding 2031608k swap on /dev/VolGroup00/LogVol02. Priority:-1 extents:1 across:2031608k SELinux: initialized (dev binfmt_misc, type binfmt_misc), uses genfs_contexts IA-32 Microcode Update Driver: v1.14a tigran@veritas.com microcode: CPU2 updated from revision 0x14 to 0x29, date = 08112004 microcode: CPU1 updated from revision 0x14 to 0x29, date = 08112004 microcode: CPU3 updated from revision 0x14 to 0x29, date = 08112004 microcode: CPU0 updated from revision 0x14 to 0x29, date = 08112004 ip6_tables: (C) 2000-2006 Netfilter Core Team ip_tables: (C) 2000-2006 Netfilter Core Team Netfilter messages via NETLINK v0.30. ip_conntrack version 2.4 (8187 buckets, 65496 max) - 228 bytes per conntrack ADDRCONF(NETDEV_UP): eth0: link is not ready e100: eth0: e100_watchdog: link up, 100Mbps, full-duplex ADDRCONF(NETDEV_CHANGE): eth0: link becomes ready libafs: module license 'http://www.openafs.org/dl/license10.html' taints kernel. Found system call table at 0xc06154e0 (pattern scan) Address 0xc06154e0 is not writable. System call hooks will not be installed; proceeding anyway enabling dynamically allocated vcaches Starting AFS cache scan...found 677 non-empty cache files (8%). SELinux: initialized (dev afs, type afs), uses genfs_contexts eth0: no IPv6 routers present SELinux: initialized (dev rpc_pipefs, type rpc_pipefs), uses genfs_contexts Bluetooth: Core ver 2.10 NET: Registered protocol family 31 Bluetooth: HCI device and connection manager initialized Bluetooth: HCI socket layer initialized Bluetooth: L2CAP ver 2.8 Bluetooth: L2CAP socket layer initialized Bluetooth: RFCOMM socket layer initialized Bluetooth: RFCOMM TTY layer initialized Bluetooth: RFCOMM ver 1.8 Bluetooth: HIDP (Human Interface Emulation) ver 1.1 SELinux: initialized (dev autofs, type autofs), uses genfs_contexts SELinux: initialized (dev autofs, type autofs), uses genfs_contexts SELinux: initialized (dev autofs, type autofs), uses genfs_contexts hdd: No disk in drive
2009/8/10 Pedro Paulo de Magalhães Oliveira Junior ppj@netfilter.com.br Can you post the output of dmesg command
----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br --- Em breve Netfilter Small Business 2009/8/10 corinna bauer <corinnab83@gmail.com> That didn't work. Corinna 2009/8/10 Pedro Paulo de Magalhães Oliveira Junior <ppj@netfilter.com.br> try: setenv doublebufferflag 1 before running tksurfer ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br --- Em breve Netfilter Small Business 2009/8/10 corinna bauer <corinnab83@gmail.com> When I run tksurfer, only portions of the cuneus, lateral occipital, and superior parietal regions are displayed. This occurs in both FS versions 4.2.0 and 4.4.0. I am using a 32 bit BU Linux system which is equivalent to redhat 5.0. The error message is similar to those in previous posts, but previous suggestions don't seem to help. surfer: current subjects dir: /home/freesurfer4.2.0/subjects/corinna/PET surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/freesurfer4.2.0/subjects/corinna/PET surfer: Reading header info from /home/freesurfer4.2.0/subjects/corinna/PET/003_S_1059/mri/T1.mgz surfer: vertices=119899, faces=239794 Loading /home/freesurfer4.2.0/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(003_S_1059) surfer: using interface /home/freesurfer4.2.0/lib/tcl/tksurfer.tcl Reading /home/freesurfer4.2.0/lib/tcl/tkm_common.tcl Reading /home/freesurfer4.2.0/lib/tcl/tkm_wrappers.tcl Reading /home/freesurfer4.2.0/lib/tcl/fsgdfPlot.tcl Reading /home/freesurfer4.2.0/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The graphics card is: nVidia Corporation NV34 [GeForce FX 5200] (rev a1). As far as I know it is the most current driver available.
2009/8/10 Nick Schmansky nicks@nmr.mgh.harvard.edu
what is the graphics card, and is the driver the most current available?
On Mon, 2009-08-10 at 17:28 -0400, corinna bauer wrote:
The output from dmesg is:
Linux version 2.6.18-128.1.14.el5 (mockbuild@builder16.centos.org) (gcc version 4.1.2 20080704 (Red Hat 4.1.2-44)) #1 SMP Wed Jun 17 06:40:54 EDT 2009 BIOS-provided physical RAM map: BIOS-e820: 0000000000000000 - 000000000009b800 (usable) BIOS-e820: 000000000009b800 - 00000000000a0000 (reserved) BIOS-e820: 00000000000e0000 - 0000000000100000 (reserved) BIOS-e820: 0000000000100000 - 000000003ff70000 (usable) BIOS-e820: 000000003ff70000 - 000000003ff7b000 (ACPI data) BIOS-e820: 000000003ff7b000 - 000000003ff80000 (ACPI NVS) BIOS-e820: 000000003ff80000 - 0000000040000000 (reserved) BIOS-e820: 00000000fec00000 - 00000000fec10000 (reserved) BIOS-e820: 00000000fee00000 - 00000000fee01000 (reserved) BIOS-e820: 00000000ff800000 - 00000000ffc00000 (reserved) BIOS-e820: 00000000fff00000 - 0000000100000000 (reserved) 127MB HIGHMEM available. 896MB LOWMEM available. found SMP MP-table at 000f6120 Memory for crash kernel (0x0 to 0x0) notwithin permissible range disabling kdump Using x86 segment limits to approximate NX protection On node 0 totalpages: 262000 DMA zone: 4096 pages, LIFO batch:0 Normal zone: 225280 pages, LIFO batch:31 HighMem zone: 32624 pages, LIFO batch:7 DMI present. Using APIC driver default ACPI: RSDP (v000 PTLTD ) @ 0x000f6160 ACPI: RSDT (v001 PTLTD RSDT 0x06040000 LTP 0x00000000) @ 0x3ff76ee4 ACPI: FADT (v001 INTEL E7505 0x06040000 PTL 0x00000008) @ 0x3ff7ae78 ACPI: MADT (v001 PTLTD APIC 0x06040000 LTP 0x00000000) @ 0x3ff7aeec ACPI: BOOT (v001 PTLTD $SBFTBL$ 0x06040000 LTP 0x00000001) @ 0x3ff7af88 ACPI: SPCR (v001 PTLTD $UCRTBL$ 0x06040000 PTL 0x00000001) @ 0x3ff7afb0 ACPI: DSDT (v001 INTEL E7505 0x06040000 MSFT 0x0100000e) @ 0x00000000 ACPI: PM-Timer IO Port: 0x1008 ACPI: Local APIC address 0xfee00000 ACPI: LAPIC (acpi_id[0x00] lapic_id[0x00] enabled) Processor #0 15:2 APIC version 20 ACPI: LAPIC (acpi_id[0x01] lapic_id[0x06] enabled) Processor #6 15:2 APIC version 20 ACPI: LAPIC (acpi_id[0x02] lapic_id[0x01] enabled) Processor #1 15:2 APIC version 20 ACPI: LAPIC (acpi_id[0x03] lapic_id[0x07] enabled) Processor #7 15:2 APIC version 20 ACPI: LAPIC_NMI (acpi_id[0x00] high edge lint[0x1]) ACPI: LAPIC_NMI (acpi_id[0x01] high edge lint[0x1]) ACPI: LAPIC_NMI (acpi_id[0x02] high edge lint[0x1]) ACPI: LAPIC_NMI (acpi_id[0x03] high edge lint[0x1]) ACPI: IOAPIC (id[0x02] address[0xfec00000] gsi_base[0]) IOAPIC[0]: apic_id 2, version 32, address 0xfec00000, GSI 0-23 ACPI: IOAPIC (id[0x03] address[0xfec80000] gsi_base[24]) IOAPIC[1]: apic_id 3, version 32, address 0xfec80000, GSI 24-47 ACPI: IOAPIC (id[0x04] address[0xfec80400] gsi_base[48]) IOAPIC[2]: apic_id 4, version 32, address 0xfec80400, GSI 48-71 ACPI: INT_SRC_OVR (bus 0 bus_irq 0 global_irq 2 high edge) ACPI: INT_SRC_OVR (bus 0 bus_irq 9 global_irq 9 high level) ACPI: IRQ0 used by override. ACPI: IRQ2 used by override. ACPI: IRQ9 used by override. Enabling APIC mode: Flat. Using 3 I/O APICs Using ACPI (MADT) for SMP configuration information Allocating PCI resources starting at 50000000 (gap: 40000000:bec00000) Detected 2392.198 MHz processor. Built 1 zonelists. Total pages: 262000 Kernel command line: ro root=/dev/VolGroup00/LogVol00 rhgb mapped APIC to ffffd000 (fee00000) mapped IOAPIC to ffffc000 (fec00000) mapped IOAPIC to ffffb000 (fec80000) mapped IOAPIC to ffffa000 (fec80400) Enabling fast FPU save and restore... done. Enabling unmasked SIMD FPU exception support... done. Initializing CPU#0 CPU 0 irqstacks, hard=c0755000 soft=c0735000 PID hash table entries: 4096 (order: 12, 16384 bytes) Console: colour VGA+ 80x25 Dentry cache hash table entries: 131072 (order: 7, 524288 bytes) Inode-cache hash table entries: 65536 (order: 6, 262144 bytes) Memory: 1030992k/1048000k available (2124k kernel code, 16344k reserved, 885k data, 228k init, 130496k highmem) Checking if this processor honours the WP bit even in supervisor mode... Ok. Calibrating delay using timer specific routine.. 4786.48 BogoMIPS (lpj=2393244) Security Framework v1.0.0 initialized SELinux: Initializing. SELinux: Starting in permissive mode selinux_register_security: Registering secondary module capability Capability LSM initialized as secondary Mount-cache hash table entries: 512 CPU: After generic identify, caps: bfebfbff 00000000 00000000 00000000 00004400 00000000 00000000 CPU: After vendor identify, caps: bfebfbff 00000000 00000000 00000000 00004400 00000000 00000000 CPU: Trace cache: 12K uops, L1 D cache: 8K CPU: L2 cache: 512K CPU: Physical Processor ID: 0 CPU: After all inits, caps: bfebf3ff 00000000 00000000 00000080 00004400 00000000 00000000 Intel machine check architecture supported. Intel machine check reporting enabled on CPU#0. CPU0: Intel P4/Xeon Extended MCE MSRs (12) available CPU0: Thermal monitoring enabled Checking 'hlt' instruction... OK. SMP alternatives: switching to UP code ACPI: Core revision 20060707 CPU0: Intel(R) Xeon(TM) CPU 2.40GHz stepping 05 SMP alternatives: switching to SMP code Booting processor 1/1 eip 3000 CPU 1 irqstacks, hard=c0756000 soft=c0736000 Initializing CPU#1 Calibrating delay using timer specific routine.. 4783.40 BogoMIPS (lpj=2391702) CPU: After generic identify, caps: bfebfbff 00000000 00000000 00000000 00004400 00000000 00000000 CPU: After vendor identify, caps: bfebfbff 00000000 00000000 00000000 00004400 00000000 00000000 CPU: Trace cache: 12K uops, L1 D cache: 8K CPU: L2 cache: 512K CPU: Physical Processor ID: 0 CPU: After all inits, caps: bfebf3ff 00000000 00000000 00000080 00004400 00000000 00000000 Intel machine check architecture supported. Intel machine check reporting enabled on CPU#1. CPU1: Intel P4/Xeon Extended MCE MSRs (12) available CPU1: Thermal monitoring enabled CPU1: Intel(R) Xeon(TM) CPU 2.40GHz stepping 05 SMP alternatives: switching to SMP code Booting processor 2/6 eip 3000 CPU 2 irqstacks, hard=c0757000 soft=c0737000 Initializing CPU#2 Calibrating delay using timer specific routine.. 4783.44 BogoMIPS (lpj=2391723) CPU: After generic identify, caps: bfebfbff 00000000 00000000 00000000 00004400 00000000 00000000 CPU: After vendor identify, caps: bfebfbff 00000000 00000000 00000000 00004400 00000000 00000000 CPU: Trace cache: 12K uops, L1 D cache: 8K CPU: L2 cache: 512K CPU: Physical Processor ID: 3 CPU: After all inits, caps: bfebf3ff 00000000 00000000 00000080 00004400 00000000 00000000 Intel machine check architecture supported. Intel machine check reporting enabled on CPU#2. CPU2: Intel P4/Xeon Extended MCE MSRs (12) available CPU2: Thermal monitoring enabled CPU2: Intel(R) Xeon(TM) CPU 2.40GHz stepping 05 SMP alternatives: switching to SMP code Booting processor 3/7 eip 3000 CPU 3 irqstacks, hard=c0758000 soft=c0738000 Initializing CPU#3 Calibrating delay using timer specific routine.. 4783.42 BogoMIPS (lpj=2391714) CPU: After generic identify, caps: bfebfbff 00000000 00000000 00000000 00004400 00000000 00000000 CPU: After vendor identify, caps: bfebfbff 00000000 00000000 00000000 00004400 00000000 00000000 CPU: Trace cache: 12K uops, L1 D cache: 8K CPU: L2 cache: 512K CPU: Physical Processor ID: 3 CPU: After all inits, caps: bfebf3ff 00000000 00000000 00000080 00004400 00000000 00000000 Intel machine check architecture supported. Intel machine check reporting enabled on CPU#3. CPU3: Intel P4/Xeon Extended MCE MSRs (12) available CPU3: Thermal monitoring enabled CPU3: Intel(R) Xeon(TM) CPU 2.40GHz stepping 05 Total of 4 processors activated (19136.76 BogoMIPS). ENABLING IO-APIC IRQs ..TIMER: vector=0x31 apic1=0 pin1=2 apic2=-1 pin2=-1 checking TSC synchronization across 4 CPUs: passed. Brought up 4 CPUs sizeof(vma)=84 bytes sizeof(page)=32 bytes sizeof(inode)=340 bytes sizeof(dentry)=136 bytes sizeof(ext3inode)=492 bytes sizeof(buffer_head)=52 bytes sizeof(skbuff)=172 bytes migration_cost=61,655 checking if image is initramfs... it is Freeing initrd memory: 3130k freed NET: Registered protocol family 16 No dock devices found. ACPI: bus type pci registered PCI: PCI BIOS revision 2.10 entry at 0xfd8f5, last bus=5 PCI: Using configuration type 1 Setting up standard PCI resources ACPI: Interpreter enabled ACPI: Using IOAPIC for interrupt routing ACPI: PCI Root Bridge [PCI0] (0000:00)
- The chipset may have PM-Timer Bug. Due to workarounds for a bug,
- this clock source is slow. If you are sure your timer does not have
- this bug, please use "acpi_pm_good" to disable the workaround
PCI quirk: region 1000-107f claimed by ICH4 ACPI/GPIO/TCO PCI quirk: region 1180-11bf claimed by ICH4 GPIO PCI: Ignoring BAR0-3 of IDE controller 0000:00:1f.1 Boot video device is 0000:01:00.0 PCI: Firmware left 0000:05:03.0 e100 interrupts enabled, disabling PCI: Transparent bridge - 0000:00:1e.0 ACPI: PCI Interrupt Routing Table [_SB_.PCI0._PRT] ACPI: PCI Interrupt Link [LNKA] (IRQs 3 4 5 7 10 *11 14 15) ACPI: PCI Interrupt Link [LNKB] (IRQs 3 4 5 7 10 11 14 15) *0, disabled. ACPI: PCI Interrupt Link [LNKC] (IRQs 3 4 *5 7 10 11 14 15) ACPI: PCI Interrupt Link [LNKD] (IRQs 3 4 5 7 *10 11 14 15) ACPI: PCI Interrupt Link [LNKE] (IRQs 3 4 5 7 10 *11 14 15) ACPI: PCI Interrupt Link [LNKF] (IRQs 3 4 5 7 10 11 14 15) *0, disabled. ACPI: PCI Interrupt Link [LNKG] (IRQs 3 4 5 7 10 *11 14 15) ACPI: PCI Interrupt Link [LNKH] (IRQs 3 4 5 7 10 *11 14 15) ACPI: PCI Interrupt Routing Table [_SB_.PCI0.ICH4._PRT] ACPI: PCI Interrupt Routing Table [_SB_.PCI0.HLB_.Z000._PRT] ACPI: PCI Interrupt Routing Table [_SB_.PCI0.HLB_.Z001._PRT] ACPI: PCI Interrupt Routing Table [_SB_.PCI0.AGP_._PRT] Linux Plug and Play Support v0.97 (c) Adam Belay pnp: PnP ACPI init pnp: PnP ACPI: found 13 devices usbcore: registered new driver usbfs usbcore: registered new driver hub PCI: Using ACPI for IRQ routing PCI: If a device doesn't work, try "pci=routeirq". If it helps, post a report NetLabel: Initializing NetLabel: domain hash size = 128 NetLabel: protocols = UNLABELED CIPSOv4 NetLabel: unlabeled traffic allowed by default PCI: mem resource #6:20000@f8000000 for 0000:01:00.0 was not allocated. PCI: Bridge: 0000:00:01.0 IO window: disabled. MEM window: d1000000-d1ffffff PREFETCH window: f0000000-f7ffffff PCI: Bridge: 0000:02:1d.0 IO window: disabled. MEM window: disabled. PREFETCH window: disabled. PCI: Bridge: 0000:02:1f.0 IO window: 7000-7fff MEM window: d2100000-d21fffff PREFETCH window: disabled. PCI: Bridge: 0000:00:02.0 IO window: 7000-7fff MEM window: d2000000-d21fffff PREFETCH window: disabled. PCI: Bridge: 0000:00:1e.0 IO window: 8000-8fff MEM window: d2200000-d22fffff PREFETCH window: disabled. PCI: Setting latency timer of device 0000:00:1e.0 to 64 NET: Registered protocol family 2 IP route cache hash table entries: 32768 (order: 5, 131072 bytes) TCP established hash table entries: 131072 (order: 8, 1048576 bytes) TCP bind hash table entries: 65536 (order: 7, 524288 bytes) TCP: Hash tables configured (established 131072 bind 65536) TCP reno registered Simple Boot Flag at 0x35 set to 0x80 apm: BIOS not found. audit: initializing netlink socket (disabled) type=2000 audit(1249916375.100:1): initialized highmem bounce pool size: 64 pages Total HugeTLB memory allocated, 0 VFS: Disk quotas dquot_6.5.1 Dquot-cache hash table entries: 1024 (order 0, 4096 bytes) SELinux: Registering netfilter hooks Initializing Cryptographic API alg: No test for crc32c (crc32c-generic) ksign: Installing public key data Loading keyring
- Added public key E5930ADED89DE961
- User ID: CentOS (Kernel Module GPG key)
io scheduler noop registered io scheduler anticipatory registered io scheduler deadline registered io scheduler cfq registered (default) pci_hotplug: PCI Hot Plug PCI Core version: 0.5 Real Time Clock Driver v1.12ac Non-volatile memory driver v1.2 Linux agpgart interface v0.101 (c) Dave Jones agpgart: Detected an Intel E7505 Chipset. agpgart: AGP aperture is 256M @ 0xe0000000 Serial: 8250/16550 driver $Revision: 1.90 $ 4 ports, IRQ sharing enabled serial8250: ttyS0 at I/O 0x3f8 (irq = 4) is a 16550A serial8250: ttyS1 at I/O 0x2f8 (irq = 3) is a 16550A 00:0a: ttyS0 at I/O 0x3f8 (irq = 4) is a 16550A 00:0b: ttyS1 at I/O 0x2f8 (irq = 3) is a 16550A RAMDISK driver initialized: 16 RAM disks of 16384K size 4096 blocksize Uniform Multi-Platform E-IDE driver Revision: 7.00alpha2 ide: Assuming 33MHz system bus speed for PIO modes; override with idebus=xx ICH4: IDE controller at PCI slot 0000:00:1f.1 PCI: Enabling device 0000:00:1f.1 (0005 -> 0007) ACPI: PCI Interrupt 0000:00:1f.1[A] -> GSI 18 (level, low) -> IRQ 169 ICH4: chipset revision 2 ICH4: not 100% native mode: will probe irqs later ide0: BM-DMA at 0x6860-0x6867, BIOS settings: hda:DMA, hdb:DMA ide1: BM-DMA at 0x6868-0x686f, BIOS settings: hdc:DMA, hdd:DMA Probing IDE interface ide0... hda: WDC WD800JB-00ETA0, ATA DISK drive hdb: WDC WD10EADS-00L5B1, ATA DISK drive ide0 at 0x1f0-0x1f7,0x3f6 on irq 14 Probing IDE interface ide1... hdc: LITE-ON LTR-52327S, ATAPI CD/DVD-ROM drive hdd: IOMEGA ZIP 250 ATAPI, ATAPI FLOPPY drive ide1 at 0x170-0x177,0x376 on irq 15 hda: max request size: 512KiB hda: 156301488 sectors (80026 MB) w/8192KiB Cache, CHS=16383/255/63, UDMA(100) hda: cache flushes supported hda: hda1 hda2 hdb: max request size: 512KiB hdb: 1953525168 sectors (1000204 MB) w/32767KiB Cache, CHS=65535/255/63, UDMA(100) hdb: cache flushes supported hdb: hdb1 ide-floppy driver 0.99.newide hdd: No disk in drive hdd: 0kB, 0/64/32 CHS, 4096 kBps, 512 sector size, 2941 rpm usbcore: registered new driver hiddev usbcore: registered new driver usbhid drivers/usb/input/hid-core.c: v2.6:USB HID core driver PNP: PS/2 Controller [PNP0303:PS2K,PNP0f13:PS2M] at 0x60,0x64 irq 1,12 serio: i8042 KBD port at 0x60,0x64 irq 1 serio: i8042 AUX port at 0x60,0x64 irq 12 mice: PS/2 mouse device common for all mice md: md driver 0.90.3 MAX_MD_DEVS=256, MD_SB_DISKS=27 md: bitmap version 4.39 TCP bic registered Initializing IPsec netlink socket NET: Registered protocol family 1 NET: Registered protocol family 17 Using IPI No-Shortcut mode ACPI: (supports S0<6>Time: tsc clocksource has been installed. S1 S4 S5) Freeing unused kernel memory: 228k freed Write protecting the kernel read-only data: 397k ACPI: PCI Interrupt 0000:00:1d.7[D] -> GSI 23 (level, low) -> IRQ 177 PCI: Setting latency timer of device 0000:00:1d.7 to 64 ehci_hcd 0000:00:1d.7: EHCI Host Controller ehci_hcd 0000:00:1d.7: new USB bus registered, assigned bus number 1 ehci_hcd 0000:00:1d.7: debug port 1 PCI: cache line size of 128 is not supported by device 0000:00:1d.7 ehci_hcd 0000:00:1d.7: irq 177, io mem 0xd0000000 ehci_hcd 0000:00:1d.7: USB 2.0 started, EHCI 1.00, driver 10 Dec 2004 usb usb1: configuration #1 chosen from 1 choice hub 1-0:1.0: USB hub found hub 1-0:1.0: 6 ports detected ohci_hcd: 2005 April 22 USB 1.1 'Open' Host Controller (OHCI) Driver (PCI) USB Universal Host Controller Interface driver v3.0 ACPI: PCI Interrupt 0000:00:1d.0[A] -> GSI 16 (level, low) -> IRQ 185 PCI: Setting latency timer of device 0000:00:1d.0 to 64 uhci_hcd 0000:00:1d.0: UHCI Host Controller uhci_hcd 0000:00:1d.0: new USB bus registered, assigned bus number 2 uhci_hcd 0000:00:1d.0: irq 185, io base 0x00006800 usb usb2: configuration #1 chosen from 1 choice hub 2-0:1.0: USB hub found hub 2-0:1.0: 2 ports detected ACPI: PCI Interrupt 0000:00:1d.1[B] -> GSI 19 (level, low) -> IRQ 193 PCI: Setting latency timer of device 0000:00:1d.1 to 64 uhci_hcd 0000:00:1d.1: UHCI Host Controller uhci_hcd 0000:00:1d.1: new USB bus registered, assigned bus number 3 uhci_hcd 0000:00:1d.1: irq 193, io base 0x00006820 usb usb3: configuration #1 chosen from 1 choice hub 3-0:1.0: USB hub found hub 3-0:1.0: 2 ports detected ACPI: PCI Interrupt 0000:00:1d.2[C] -> GSI 18 (level, low) -> IRQ 169 PCI: Setting latency timer of device 0000:00:1d.2 to 64 uhci_hcd 0000:00:1d.2: UHCI Host Controller uhci_hcd 0000:00:1d.2: new USB bus registered, assigned bus number 4 uhci_hcd 0000:00:1d.2: irq 169, io base 0x00006840 usb usb4: configuration #1 chosen from 1 choice hub 4-0:1.0: USB hub found hub 4-0:1.0: 2 ports detected hdd: No disk in drive usb 2-1: new low speed USB device using uhci_hcd and address 2 usb 2-1: configuration #1 chosen from 1 choice input: Rextron USB as /class/input/input0 input: USB HID v1.00 Keyboard [Rextron USB] on usb-0000:00:1d.0-1 input: Rextron USB as /class/input/input1 input: USB HID v1.10 Mouse [Rextron USB] on usb-0000:00:1d.0-1 SCSI subsystem initialized libata version 3.00 loaded. device-mapper: uevent: version 1.0.3 device-mapper: ioctl: 4.11.5-ioctl (2007-12-12) initialised: dm-devel@redhat.com device-mapper: dm-raid45: initialized v0.2429 hdd: No disk in drive hdd: No disk in drive hdd: No disk in drive hdd: No disk in drive kjournald starting. Commit interval 5 seconds EXT3-fs: mounted filesystem with ordered data mode. security: 3 users, 6 roles, 1914 types, 234 bools, 1 sens, 1024 cats security: 61 classes, 69080 rules SELinux: Completing initialization. SELinux: Setting up existing superblocks. SELinux: initialized (dev dm-0, type ext3), uses xattr SELinux: initialized (dev usbfs, type usbfs), uses genfs_contexts SELinux: initialized (dev tmpfs, type tmpfs), uses transition SIDs SELinux: initialized (dev debugfs, type debugfs), uses genfs_contexts SELinux: initialized (dev selinuxfs, type selinuxfs), uses genfs_contexts SELinux: initialized (dev mqueue, type mqueue), uses transition SIDs SELinux: initialized (dev hugetlbfs, type hugetlbfs), uses genfs_contexts SELinux: initialized (dev devpts, type devpts), uses transition SIDs SELinux: initialized (dev eventpollfs, type eventpollfs), uses task SIDs SELinux: initialized (dev inotifyfs, type inotifyfs), uses genfs_contexts SELinux: initialized (dev tmpfs, type tmpfs), uses transition SIDs SELinux: initialized (dev futexfs, type futexfs), uses genfs_contexts SELinux: initialized (dev anon_inodefs, type anon_inodefs), uses genfs_contexts SELinux: initialized (dev pipefs, type pipefs), uses task SIDs SELinux: initialized (dev sockfs, type sockfs), uses task SIDs SELinux: initialized (dev cpuset, type cpuset), uses genfs_contexts SELinux: initialized (dev proc, type proc), uses genfs_contexts SELinux: initialized (dev bdev, type bdev), uses genfs_contexts SELinux: initialized (dev rootfs, type rootfs), uses genfs_contexts SELinux: initialized (dev sysfs, type sysfs), uses genfs_contexts type=1403 audit(1249916400.115:2): policy loaded auid=4294967295 ses=4294967295 e100: Intel(R) PRO/100 Network Driver, 3.5.10-k2-NAPI e100: Copyright(c) 1999-2005 Intel Corporation ACPI: PCI Interrupt 0000:05:03.0[A] -> GSI 18 (level, low) -> IRQ 169 e100: eth0: e100_probe: addr 0xd2220000, irq 169, MAC addr 00:04:23:88:86:55 Intel(R) PRO/1000 Network Driver - version 7.3.20-k2-NAPI Copyright (c) 1999-2006 Intel Corporation. ACPI: PCI Interrupt 0000:04:02.0[A] -> GSI 52 (level, low) -> IRQ 201 e1000: 0000:04:02.0: e1000_probe: (PCI:66MHz:32-bit) 00:04:23:88:87:43 e1000: eth1: e1000_probe: Intel(R) PRO/1000 Network Connection hdc: ATAPI 52X CD-ROM CD-R/RW drive, 2048kB Cache, UDMA(33) Uniform CD-ROM driver Revision: 3.20 gameport: EMU10K1 is pci0000:05:01.1/gameport0, io 0x8060, speed 962kHz parport: PnPBIOS parport detected. parport0: PC-style at 0x378 (0x778), irq 7 [PCSPP,TRISTATE,EPP] ACPI: PCI Interrupt 0000:00:1f.3[B] -> GSI 17 (level, low) -> IRQ 209 input: PC Speaker as /class/input/input2 Floppy drive(s): fd0 is 1.44M EDAC MC: Ver: 2.0.1 Jun 17 2009 FDC 0 is a post-1991 82077 ACPI: PCI Interrupt 0000:05:01.0[A] -> GSI 22 (level, low) -> IRQ 217 lp0: using parport0 (interrupt-driven). lp0: console ready SELinux: initialized (dev ramfs, type ramfs), uses genfs_contexts NET: Registered protocol family 10 lo: Disabled Privacy Extensions IPv6 over IPv4 tunneling driver ACPI: Power Button (FF) [PWRF] ACPI: Power Button (CM) [PWRB] md: Autodetecting RAID arrays. md: autorun ... md: ... autorun DONE. device-mapper: multipath: version 1.0.5 loaded EXT3 FS on dm-0, internal journal kjournald starting. Commit interval 5 seconds EXT3 FS on dm-1, internal journal EXT3-fs: mounted filesystem with ordered data mode. SELinux: initialized (dev dm-1, type ext3), uses xattr kjournald starting. Commit interval 5 seconds EXT3 FS on hda1, internal journal EXT3-fs: mounted filesystem with ordered data mode. SELinux: initialized (dev hda1, type ext3), uses xattr SELinux: initialized (dev tmpfs, type tmpfs), uses transition SIDs Adding 2031608k swap on /dev/VolGroup00/LogVol02. Priority:-1 extents:1 across:2031608k SELinux: initialized (dev binfmt_misc, type binfmt_misc), uses genfs_contexts IA-32 Microcode Update Driver: v1.14a tigran@veritas.com microcode: CPU2 updated from revision 0x14 to 0x29, date = 08112004 microcode: CPU1 updated from revision 0x14 to 0x29, date = 08112004 microcode: CPU3 updated from revision 0x14 to 0x29, date = 08112004 microcode: CPU0 updated from revision 0x14 to 0x29, date = 08112004 ip6_tables: (C) 2000-2006 Netfilter Core Team ip_tables: (C) 2000-2006 Netfilter Core Team Netfilter messages via NETLINK v0.30. ip_conntrack version 2.4 (8187 buckets, 65496 max) - 228 bytes per conntrack ADDRCONF(NETDEV_UP): eth0: link is not ready e100: eth0: e100_watchdog: link up, 100Mbps, full-duplex ADDRCONF(NETDEV_CHANGE): eth0: link becomes ready libafs: module license 'http://www.openafs.org/dl/license10.html' taints kernel. Found system call table at 0xc06154e0 (pattern scan) Address 0xc06154e0 is not writable. System call hooks will not be installed; proceeding anyway enabling dynamically allocated vcaches Starting AFS cache scan...found 677 non-empty cache files (8%). SELinux: initialized (dev afs, type afs), uses genfs_contexts eth0: no IPv6 routers present SELinux: initialized (dev rpc_pipefs, type rpc_pipefs), uses genfs_contexts Bluetooth: Core ver 2.10 NET: Registered protocol family 31 Bluetooth: HCI device and connection manager initialized Bluetooth: HCI socket layer initialized Bluetooth: L2CAP ver 2.8 Bluetooth: L2CAP socket layer initialized Bluetooth: RFCOMM socket layer initialized Bluetooth: RFCOMM TTY layer initialized Bluetooth: RFCOMM ver 1.8 Bluetooth: HIDP (Human Interface Emulation) ver 1.1 SELinux: initialized (dev autofs, type autofs), uses genfs_contexts SELinux: initialized (dev autofs, type autofs), uses genfs_contexts SELinux: initialized (dev autofs, type autofs), uses genfs_contexts hdd: No disk in drive
2009/8/10 Pedro Paulo de Magalhães Oliveira Junior ppj@netfilter.com.br Can you post the output of dmesg command
----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br --- Em breve Netfilter Small Business 2009/8/10 corinna bauer <corinnab83@gmail.com> That didn't work. Corinna 2009/8/10 Pedro Paulo de Magalhães Oliveira Junior <ppj@netfilter.com.br> try: setenv doublebufferflag 1 before running tksurfer
Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br --- Em breve Netfilter Small Business 2009/8/10 corinna bauer <corinnab83@gmail.com> When I run tksurfer, only portions of the cuneus, lateral occipital, and superior parietal regions are displayed. This occurs in both FS versions 4.2.0 and 4.4.0. I am using a 32 bit BU Linux system which is equivalent to redhat 5.0. The error message is similar to those in previous posts, but previous suggestions don't seem to help. surfer: current subjects dir:/home/freesurfer4.2.0/subjects/corinna/PET
surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer:/home/freesurfer4.2.0/subjects/corinna/PET
surfer: Reading header info from/home/freesurfer4.2.0/subjects/corinna/PET/003_S_1059/mri/T1.mgz
surfer: vertices=119899, faces=239794 Loading/home/freesurfer4.2.0/surface_labels.txt
surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(003_S_1059) surfer: using interface/home/freesurfer4.2.0/lib/tcl/tksurfer.tcl
Reading/home/freesurfer4.2.0/lib/tcl/tkm_common.tcl
Reading/home/freesurfer4.2.0/lib/tcl/tkm_wrappers.tcl
Reading/home/freesurfer4.2.0/lib/tcl/fsgdfPlot.tcl
Reading/home/freesurfer4.2.0/lib/tcl/tkUtils.tcl
Successfully parsed tksurfer.tcl reading white matter vertex locations...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Corinna,
run this to ensure the driver is up-to-date:
sudo /sbin/init 3 <CR> to get login prompt login sudo /usr/bin/nvidia-installer update
Nick
On Tue, 2009-08-11 at 10:01 -0400, corinna bauer wrote:
The graphics card is: nVidia Corporation NV34 [GeForce FX 5200] (rev a1). As far as I know it is the most current driver available.
2009/8/10 Nick Schmansky nicks@nmr.mgh.harvard.edu what is the graphics card, and is the driver the most current available?
On Mon, 2009-08-10 at 17:28 -0400, corinna bauer wrote: > The output from dmesg is: > > Linux version 2.6.18-128.1.14.el5 (mockbuild@builder16.centos.org) > (gcc version 4.1.2 20080704 (Red Hat 4.1.2-44)) #1 SMP Wed Jun 17 > 06:40:54 EDT 2009 > BIOS-provided physical RAM map: > BIOS-e820: 0000000000000000 - 000000000009b800 (usable) > BIOS-e820: 000000000009b800 - 00000000000a0000 (reserved) > BIOS-e820: 00000000000e0000 - 0000000000100000 (reserved) > BIOS-e820: 0000000000100000 - 000000003ff70000 (usable) > BIOS-e820: 000000003ff70000 - 000000003ff7b000 (ACPI data) > BIOS-e820: 000000003ff7b000 - 000000003ff80000 (ACPI NVS) > BIOS-e820: 000000003ff80000 - 0000000040000000 (reserved) > BIOS-e820: 00000000fec00000 - 00000000fec10000 (reserved) > BIOS-e820: 00000000fee00000 - 00000000fee01000 (reserved) > BIOS-e820: 00000000ff800000 - 00000000ffc00000 (reserved) > BIOS-e820: 00000000fff00000 - 0000000100000000 (reserved) > 127MB HIGHMEM available. > 896MB LOWMEM available. > found SMP MP-table at 000f6120 > Memory for crash kernel (0x0 to 0x0) notwithin permissible range > disabling kdump > Using x86 segment limits to approximate NX protection > On node 0 totalpages: 262000 > DMA zone: 4096 pages, LIFO batch:0 > Normal zone: 225280 pages, LIFO batch:31 > HighMem zone: 32624 pages, LIFO batch:7 > DMI present. > Using APIC driver default > ACPI: RSDP (v000 PTLTD ) @ 0x000f6160 > ACPI: RSDT (v001 PTLTD RSDT 0x06040000 LTP 0x00000000) @ > 0x3ff76ee4 > ACPI: FADT (v001 INTEL E7505 0x06040000 PTL 0x00000008) @ > 0x3ff7ae78 > ACPI: MADT (v001 PTLTD APIC 0x06040000 LTP 0x00000000) @ > 0x3ff7aeec > ACPI: BOOT (v001 PTLTD $SBFTBL$ 0x06040000 LTP 0x00000001) @ > 0x3ff7af88 > ACPI: SPCR (v001 PTLTD $UCRTBL$ 0x06040000 PTL 0x00000001) @ > 0x3ff7afb0 > ACPI: DSDT (v001 INTEL E7505 0x06040000 MSFT 0x0100000e) @ > 0x00000000 > ACPI: PM-Timer IO Port: 0x1008 > ACPI: Local APIC address 0xfee00000 > ACPI: LAPIC (acpi_id[0x00] lapic_id[0x00] enabled) > Processor #0 15:2 APIC version 20 > ACPI: LAPIC (acpi_id[0x01] lapic_id[0x06] enabled) > Processor #6 15:2 APIC version 20 > ACPI: LAPIC (acpi_id[0x02] lapic_id[0x01] enabled) > Processor #1 15:2 APIC version 20 > ACPI: LAPIC (acpi_id[0x03] lapic_id[0x07] enabled) > Processor #7 15:2 APIC version 20 > ACPI: LAPIC_NMI (acpi_id[0x00] high edge lint[0x1]) > ACPI: LAPIC_NMI (acpi_id[0x01] high edge lint[0x1]) > ACPI: LAPIC_NMI (acpi_id[0x02] high edge lint[0x1]) > ACPI: LAPIC_NMI (acpi_id[0x03] high edge lint[0x1]) > ACPI: IOAPIC (id[0x02] address[0xfec00000] gsi_base[0]) > IOAPIC[0]: apic_id 2, version 32, address 0xfec00000, GSI 0-23 > ACPI: IOAPIC (id[0x03] address[0xfec80000] gsi_base[24]) > IOAPIC[1]: apic_id 3, version 32, address 0xfec80000, GSI 24-47 > ACPI: IOAPIC (id[0x04] address[0xfec80400] gsi_base[48]) > IOAPIC[2]: apic_id 4, version 32, address 0xfec80400, GSI 48-71 > ACPI: INT_SRC_OVR (bus 0 bus_irq 0 global_irq 2 high edge) > ACPI: INT_SRC_OVR (bus 0 bus_irq 9 global_irq 9 high level) > ACPI: IRQ0 used by override. > ACPI: IRQ2 used by override. > ACPI: IRQ9 used by override. > Enabling APIC mode: Flat. Using 3 I/O APICs > Using ACPI (MADT) for SMP configuration information > Allocating PCI resources starting at 50000000 (gap: 40000000:bec00000) > Detected 2392.198 MHz processor. > Built 1 zonelists. Total pages: 262000 > Kernel command line: ro root=/dev/VolGroup00/LogVol00 rhgb > mapped APIC to ffffd000 (fee00000) > mapped IOAPIC to ffffc000 (fec00000) > mapped IOAPIC to ffffb000 (fec80000) > mapped IOAPIC to ffffa000 (fec80400) > Enabling fast FPU save and restore... done. > Enabling unmasked SIMD FPU exception support... done. > Initializing CPU#0 > CPU 0 irqstacks, hard=c0755000 soft=c0735000 > PID hash table entries: 4096 (order: 12, 16384 bytes) > Console: colour VGA+ 80x25 > Dentry cache hash table entries: 131072 (order: 7, 524288 bytes) > Inode-cache hash table entries: 65536 (order: 6, 262144 bytes) > Memory: 1030992k/1048000k available (2124k kernel code, 16344k > reserved, 885k data, 228k init, 130496k highmem) > Checking if this processor honours the WP bit even in supervisor > mode... Ok. > Calibrating delay using timer specific routine.. 4786.48 BogoMIPS > (lpj=2393244) > Security Framework v1.0.0 initialized > SELinux: Initializing. > SELinux: Starting in permissive mode > selinux_register_security: Registering secondary module capability > Capability LSM initialized as secondary > Mount-cache hash table entries: 512 > CPU: After generic identify, caps: bfebfbff 00000000 00000000 00000000 > 00004400 00000000 00000000 > CPU: After vendor identify, caps: bfebfbff 00000000 00000000 00000000 > 00004400 00000000 00000000 > CPU: Trace cache: 12K uops, L1 D cache: 8K > CPU: L2 cache: 512K > CPU: Physical Processor ID: 0 > CPU: After all inits, caps: bfebf3ff 00000000 00000000 00000080 > 00004400 00000000 00000000 > Intel machine check architecture supported. > Intel machine check reporting enabled on CPU#0. > CPU0: Intel P4/Xeon Extended MCE MSRs (12) available > CPU0: Thermal monitoring enabled > Checking 'hlt' instruction... OK. > SMP alternatives: switching to UP code > ACPI: Core revision 20060707 > CPU0: Intel(R) Xeon(TM) CPU 2.40GHz stepping 05 > SMP alternatives: switching to SMP code > Booting processor 1/1 eip 3000 > CPU 1 irqstacks, hard=c0756000 soft=c0736000 > Initializing CPU#1 > Calibrating delay using timer specific routine.. 4783.40 BogoMIPS > (lpj=2391702) > CPU: After generic identify, caps: bfebfbff 00000000 00000000 00000000 > 00004400 00000000 00000000 > CPU: After vendor identify, caps: bfebfbff 00000000 00000000 00000000 > 00004400 00000000 00000000 > CPU: Trace cache: 12K uops, L1 D cache: 8K > CPU: L2 cache: 512K > CPU: Physical Processor ID: 0 > CPU: After all inits, caps: bfebf3ff 00000000 00000000 00000080 > 00004400 00000000 00000000 > Intel machine check architecture supported. > Intel machine check reporting enabled on CPU#1. > CPU1: Intel P4/Xeon Extended MCE MSRs (12) available > CPU1: Thermal monitoring enabled > CPU1: Intel(R) Xeon(TM) CPU 2.40GHz stepping 05 > SMP alternatives: switching to SMP code > Booting processor 2/6 eip 3000 > CPU 2 irqstacks, hard=c0757000 soft=c0737000 > Initializing CPU#2 > Calibrating delay using timer specific routine.. 4783.44 BogoMIPS > (lpj=2391723) > CPU: After generic identify, caps: bfebfbff 00000000 00000000 00000000 > 00004400 00000000 00000000 > CPU: After vendor identify, caps: bfebfbff 00000000 00000000 00000000 > 00004400 00000000 00000000 > CPU: Trace cache: 12K uops, L1 D cache: 8K > CPU: L2 cache: 512K > CPU: Physical Processor ID: 3 > CPU: After all inits, caps: bfebf3ff 00000000 00000000 00000080 > 00004400 00000000 00000000 > Intel machine check architecture supported. > Intel machine check reporting enabled on CPU#2. > CPU2: Intel P4/Xeon Extended MCE MSRs (12) available > CPU2: Thermal monitoring enabled > CPU2: Intel(R) Xeon(TM) CPU 2.40GHz stepping 05 > SMP alternatives: switching to SMP code > Booting processor 3/7 eip 3000 > CPU 3 irqstacks, hard=c0758000 soft=c0738000 > Initializing CPU#3 > Calibrating delay using timer specific routine.. 4783.42 BogoMIPS > (lpj=2391714) > CPU: After generic identify, caps: bfebfbff 00000000 00000000 00000000 > 00004400 00000000 00000000 > CPU: After vendor identify, caps: bfebfbff 00000000 00000000 00000000 > 00004400 00000000 00000000 > CPU: Trace cache: 12K uops, L1 D cache: 8K > CPU: L2 cache: 512K > CPU: Physical Processor ID: 3 > CPU: After all inits, caps: bfebf3ff 00000000 00000000 00000080 > 00004400 00000000 00000000 > Intel machine check architecture supported. > Intel machine check reporting enabled on CPU#3. > CPU3: Intel P4/Xeon Extended MCE MSRs (12) available > CPU3: Thermal monitoring enabled > CPU3: Intel(R) Xeon(TM) CPU 2.40GHz stepping 05 > Total of 4 processors activated (19136.76 BogoMIPS). > ENABLING IO-APIC IRQs > ..TIMER: vector=0x31 apic1=0 pin1=2 apic2=-1 pin2=-1 > checking TSC synchronization across 4 CPUs: passed. > Brought up 4 CPUs > sizeof(vma)=84 bytes > sizeof(page)=32 bytes > sizeof(inode)=340 bytes > sizeof(dentry)=136 bytes > sizeof(ext3inode)=492 bytes > sizeof(buffer_head)=52 bytes > sizeof(skbuff)=172 bytes > migration_cost=61,655 > checking if image is initramfs... it is > Freeing initrd memory: 3130k freed > NET: Registered protocol family 16 > No dock devices found. > ACPI: bus type pci registered > PCI: PCI BIOS revision 2.10 entry at 0xfd8f5, last bus=5 > PCI: Using configuration type 1 > Setting up standard PCI resources > ACPI: Interpreter enabled > ACPI: Using IOAPIC for interrupt routing > ACPI: PCI Root Bridge [PCI0] (0000:00) > * The chipset may have PM-Timer Bug. Due to workarounds for a bug, > * this clock source is slow. If you are sure your timer does not have > * this bug, please use "acpi_pm_good" to disable the workaround > PCI quirk: region 1000-107f claimed by ICH4 ACPI/GPIO/TCO > PCI quirk: region 1180-11bf claimed by ICH4 GPIO > PCI: Ignoring BAR0-3 of IDE controller 0000:00:1f.1 > Boot video device is 0000:01:00.0 > PCI: Firmware left 0000:05:03.0 e100 interrupts enabled, disabling > PCI: Transparent bridge - 0000:00:1e.0 > ACPI: PCI Interrupt Routing Table [\_SB_.PCI0._PRT] > ACPI: PCI Interrupt Link [LNKA] (IRQs 3 4 5 7 10 *11 14 15) > ACPI: PCI Interrupt Link [LNKB] (IRQs 3 4 5 7 10 11 14 15) *0, > disabled. > ACPI: PCI Interrupt Link [LNKC] (IRQs 3 4 *5 7 10 11 14 15) > ACPI: PCI Interrupt Link [LNKD] (IRQs 3 4 5 7 *10 11 14 15) > ACPI: PCI Interrupt Link [LNKE] (IRQs 3 4 5 7 10 *11 14 15) > ACPI: PCI Interrupt Link [LNKF] (IRQs 3 4 5 7 10 11 14 15) *0, > disabled. > ACPI: PCI Interrupt Link [LNKG] (IRQs 3 4 5 7 10 *11 14 15) > ACPI: PCI Interrupt Link [LNKH] (IRQs 3 4 5 7 10 *11 14 15) > ACPI: PCI Interrupt Routing Table [\_SB_.PCI0.ICH4._PRT] > ACPI: PCI Interrupt Routing Table [\_SB_.PCI0.HLB_.Z000._PRT] > ACPI: PCI Interrupt Routing Table [\_SB_.PCI0.HLB_.Z001._PRT] > ACPI: PCI Interrupt Routing Table [\_SB_.PCI0.AGP_._PRT] > Linux Plug and Play Support v0.97 (c) Adam Belay > pnp: PnP ACPI init > pnp: PnP ACPI: found 13 devices > usbcore: registered new driver usbfs > usbcore: registered new driver hub > PCI: Using ACPI for IRQ routing > PCI: If a device doesn't work, try "pci=routeirq". If it helps, post > a report > NetLabel: Initializing > NetLabel: domain hash size = 128 > NetLabel: protocols = UNLABELED CIPSOv4 > NetLabel: unlabeled traffic allowed by default > PCI: mem resource #6:20000@f8000000 for 0000:01:00.0 was not > allocated. > PCI: Bridge: 0000:00:01.0 > IO window: disabled. > MEM window: d1000000-d1ffffff > PREFETCH window: f0000000-f7ffffff > PCI: Bridge: 0000:02:1d.0 > IO window: disabled. > MEM window: disabled. > PREFETCH window: disabled. > PCI: Bridge: 0000:02:1f.0 > IO window: 7000-7fff > MEM window: d2100000-d21fffff > PREFETCH window: disabled. > PCI: Bridge: 0000:00:02.0 > IO window: 7000-7fff > MEM window: d2000000-d21fffff > PREFETCH window: disabled. > PCI: Bridge: 0000:00:1e.0 > IO window: 8000-8fff > MEM window: d2200000-d22fffff > PREFETCH window: disabled. > PCI: Setting latency timer of device 0000:00:1e.0 to 64 > NET: Registered protocol family 2 > IP route cache hash table entries: 32768 (order: 5, 131072 bytes) > TCP established hash table entries: 131072 (order: 8, 1048576 bytes) > TCP bind hash table entries: 65536 (order: 7, 524288 bytes) > TCP: Hash tables configured (established 131072 bind 65536) > TCP reno registered > Simple Boot Flag at 0x35 set to 0x80 > apm: BIOS not found. > audit: initializing netlink socket (disabled) > type=2000 audit(1249916375.100:1): initialized > highmem bounce pool size: 64 pages > Total HugeTLB memory allocated, 0 > VFS: Disk quotas dquot_6.5.1 > Dquot-cache hash table entries: 1024 (order 0, 4096 bytes) > SELinux: Registering netfilter hooks > Initializing Cryptographic API > alg: No test for crc32c (crc32c-generic) > ksign: Installing public key data > Loading keyring > - Added public key E5930ADED89DE961 > - User ID: CentOS (Kernel Module GPG key) > io scheduler noop registered > io scheduler anticipatory registered > io scheduler deadline registered > io scheduler cfq registered (default) > pci_hotplug: PCI Hot Plug PCI Core version: 0.5 > Real Time Clock Driver v1.12ac > Non-volatile memory driver v1.2 > Linux agpgart interface v0.101 (c) Dave Jones > agpgart: Detected an Intel E7505 Chipset. > agpgart: AGP aperture is 256M @ 0xe0000000 > Serial: 8250/16550 driver $Revision: 1.90 $ 4 ports, IRQ sharing > enabled > serial8250: ttyS0 at I/O 0x3f8 (irq = 4) is a 16550A > serial8250: ttyS1 at I/O 0x2f8 (irq = 3) is a 16550A > 00:0a: ttyS0 at I/O 0x3f8 (irq = 4) is a 16550A > 00:0b: ttyS1 at I/O 0x2f8 (irq = 3) is a 16550A > RAMDISK driver initialized: 16 RAM disks of 16384K size 4096 blocksize > Uniform Multi-Platform E-IDE driver Revision: 7.00alpha2 > ide: Assuming 33MHz system bus speed for PIO modes; override with > idebus=xx > ICH4: IDE controller at PCI slot 0000:00:1f.1 > PCI: Enabling device 0000:00:1f.1 (0005 -> 0007) > ACPI: PCI Interrupt 0000:00:1f.1[A] -> GSI 18 (level, low) -> IRQ 169 > ICH4: chipset revision 2 > ICH4: not 100% native mode: will probe irqs later > ide0: BM-DMA at 0x6860-0x6867, BIOS settings: hda:DMA, hdb:DMA > ide1: BM-DMA at 0x6868-0x686f, BIOS settings: hdc:DMA, hdd:DMA > Probing IDE interface ide0... > hda: WDC WD800JB-00ETA0, ATA DISK drive > hdb: WDC WD10EADS-00L5B1, ATA DISK drive > ide0 at 0x1f0-0x1f7,0x3f6 on irq 14 > Probing IDE interface ide1... > hdc: LITE-ON LTR-52327S, ATAPI CD/DVD-ROM drive > hdd: IOMEGA ZIP 250 ATAPI, ATAPI FLOPPY drive > ide1 at 0x170-0x177,0x376 on irq 15 > hda: max request size: 512KiB > hda: 156301488 sectors (80026 MB) w/8192KiB Cache, CHS=16383/255/63, > UDMA(100) > hda: cache flushes supported > hda: hda1 hda2 > hdb: max request size: 512KiB > hdb: 1953525168 sectors (1000204 MB) w/32767KiB Cache, > CHS=65535/255/63, UDMA(100) > hdb: cache flushes supported > hdb: hdb1 > ide-floppy driver 0.99.newide > hdd: No disk in drive > hdd: 0kB, 0/64/32 CHS, 4096 kBps, 512 sector size, 2941 rpm > usbcore: registered new driver hiddev > usbcore: registered new driver usbhid > drivers/usb/input/hid-core.c: v2.6:USB HID core driver > PNP: PS/2 Controller [PNP0303:PS2K,PNP0f13:PS2M] at 0x60,0x64 irq 1,12 > serio: i8042 KBD port at 0x60,0x64 irq 1 > serio: i8042 AUX port at 0x60,0x64 irq 12 > mice: PS/2 mouse device common for all mice > md: md driver 0.90.3 MAX_MD_DEVS=256, MD_SB_DISKS=27 > md: bitmap version 4.39 > TCP bic registered > Initializing IPsec netlink socket > NET: Registered protocol family 1 > NET: Registered protocol family 17 > Using IPI No-Shortcut mode > ACPI: (supports S0<6>Time: tsc clocksource has been installed. > S1 S4 S5) > Freeing unused kernel memory: 228k freed > Write protecting the kernel read-only data: 397k > ACPI: PCI Interrupt 0000:00:1d.7[D] -> GSI 23 (level, low) -> IRQ 177 > PCI: Setting latency timer of device 0000:00:1d.7 to 64 > ehci_hcd 0000:00:1d.7: EHCI Host Controller > ehci_hcd 0000:00:1d.7: new USB bus registered, assigned bus number 1 > ehci_hcd 0000:00:1d.7: debug port 1 > PCI: cache line size of 128 is not supported by device 0000:00:1d.7 > ehci_hcd 0000:00:1d.7: irq 177, io mem 0xd0000000 > ehci_hcd 0000:00:1d.7: USB 2.0 started, EHCI 1.00, driver 10 Dec 2004 > usb usb1: configuration #1 chosen from 1 choice > hub 1-0:1.0: USB hub found > hub 1-0:1.0: 6 ports detected > ohci_hcd: 2005 April 22 USB 1.1 'Open' Host Controller (OHCI) Driver > (PCI) > USB Universal Host Controller Interface driver v3.0 > ACPI: PCI Interrupt 0000:00:1d.0[A] -> GSI 16 (level, low) -> IRQ 185 > PCI: Setting latency timer of device 0000:00:1d.0 to 64 > uhci_hcd 0000:00:1d.0: UHCI Host Controller > uhci_hcd 0000:00:1d.0: new USB bus registered, assigned bus number 2 > uhci_hcd 0000:00:1d.0: irq 185, io base 0x00006800 > usb usb2: configuration #1 chosen from 1 choice > hub 2-0:1.0: USB hub found > hub 2-0:1.0: 2 ports detected > ACPI: PCI Interrupt 0000:00:1d.1[B] -> GSI 19 (level, low) -> IRQ 193 > PCI: Setting latency timer of device 0000:00:1d.1 to 64 > uhci_hcd 0000:00:1d.1: UHCI Host Controller > uhci_hcd 0000:00:1d.1: new USB bus registered, assigned bus number 3 > uhci_hcd 0000:00:1d.1: irq 193, io base 0x00006820 > usb usb3: configuration #1 chosen from 1 choice > hub 3-0:1.0: USB hub found > hub 3-0:1.0: 2 ports detected > ACPI: PCI Interrupt 0000:00:1d.2[C] -> GSI 18 (level, low) -> IRQ 169 > PCI: Setting latency timer of device 0000:00:1d.2 to 64 > uhci_hcd 0000:00:1d.2: UHCI Host Controller > uhci_hcd 0000:00:1d.2: new USB bus registered, assigned bus number 4 > uhci_hcd 0000:00:1d.2: irq 169, io base 0x00006840 > usb usb4: configuration #1 chosen from 1 choice > hub 4-0:1.0: USB hub found > hub 4-0:1.0: 2 ports detected > hdd: No disk in drive > usb 2-1: new low speed USB device using uhci_hcd and address 2 > usb 2-1: configuration #1 chosen from 1 choice > input: Rextron USB as /class/input/input0 > input: USB HID v1.00 Keyboard [Rextron USB] on usb-0000:00:1d.0-1 > input: Rextron USB as /class/input/input1 > input: USB HID v1.10 Mouse [Rextron USB] on usb-0000:00:1d.0-1 > SCSI subsystem initialized > libata version 3.00 loaded. > device-mapper: uevent: version 1.0.3 > device-mapper: ioctl: 4.11.5-ioctl (2007-12-12) initialised: > dm-devel@redhat.com > device-mapper: dm-raid45: initialized v0.2429 > hdd: No disk in drive > hdd: No disk in drive > hdd: No disk in drive > hdd: No disk in drive > kjournald starting. Commit interval 5 seconds > EXT3-fs: mounted filesystem with ordered data mode. > security: 3 users, 6 roles, 1914 types, 234 bools, 1 sens, 1024 cats > security: 61 classes, 69080 rules > SELinux: Completing initialization. > SELinux: Setting up existing superblocks. > SELinux: initialized (dev dm-0, type ext3), uses xattr > SELinux: initialized (dev usbfs, type usbfs), uses genfs_contexts > SELinux: initialized (dev tmpfs, type tmpfs), uses transition SIDs > SELinux: initialized (dev debugfs, type debugfs), uses genfs_contexts > SELinux: initialized (dev selinuxfs, type selinuxfs), uses > genfs_contexts > SELinux: initialized (dev mqueue, type mqueue), uses transition SIDs > SELinux: initialized (dev hugetlbfs, type hugetlbfs), uses > genfs_contexts > SELinux: initialized (dev devpts, type devpts), uses transition SIDs > SELinux: initialized (dev eventpollfs, type eventpollfs), uses task > SIDs > SELinux: initialized (dev inotifyfs, type inotifyfs), uses > genfs_contexts > SELinux: initialized (dev tmpfs, type tmpfs), uses transition SIDs > SELinux: initialized (dev futexfs, type futexfs), uses genfs_contexts > SELinux: initialized (dev anon_inodefs, type anon_inodefs), uses > genfs_contexts > SELinux: initialized (dev pipefs, type pipefs), uses task SIDs > SELinux: initialized (dev sockfs, type sockfs), uses task SIDs > SELinux: initialized (dev cpuset, type cpuset), uses genfs_contexts > SELinux: initialized (dev proc, type proc), uses genfs_contexts > SELinux: initialized (dev bdev, type bdev), uses genfs_contexts > SELinux: initialized (dev rootfs, type rootfs), uses genfs_contexts > SELinux: initialized (dev sysfs, type sysfs), uses genfs_contexts > type=1403 audit(1249916400.115:2): policy loaded auid=4294967295 > ses=4294967295 > e100: Intel(R) PRO/100 Network Driver, 3.5.10-k2-NAPI > e100: Copyright(c) 1999-2005 Intel Corporation > ACPI: PCI Interrupt 0000:05:03.0[A] -> GSI 18 (level, low) -> IRQ 169 > e100: eth0: e100_probe: addr 0xd2220000, irq 169, MAC addr > 00:04:23:88:86:55 > Intel(R) PRO/1000 Network Driver - version 7.3.20-k2-NAPI > Copyright (c) 1999-2006 Intel Corporation. > ACPI: PCI Interrupt 0000:04:02.0[A] -> GSI 52 (level, low) -> IRQ 201 > e1000: 0000:04:02.0: e1000_probe: (PCI:66MHz:32-bit) 00:04:23:88:87:43 > e1000: eth1: e1000_probe: Intel(R) PRO/1000 Network Connection > hdc: ATAPI 52X CD-ROM CD-R/RW drive, 2048kB Cache, UDMA(33) > Uniform CD-ROM driver Revision: 3.20 > gameport: EMU10K1 is pci0000:05:01.1/gameport0, io 0x8060, speed > 962kHz > parport: PnPBIOS parport detected. > parport0: PC-style at 0x378 (0x778), irq 7 [PCSPP,TRISTATE,EPP] > ACPI: PCI Interrupt 0000:00:1f.3[B] -> GSI 17 (level, low) -> IRQ 209 > input: PC Speaker as /class/input/input2 > Floppy drive(s): fd0 is 1.44M > EDAC MC: Ver: 2.0.1 Jun 17 2009 > FDC 0 is a post-1991 82077 > ACPI: PCI Interrupt 0000:05:01.0[A] -> GSI 22 (level, low) -> IRQ 217 > lp0: using parport0 (interrupt-driven). > lp0: console ready > SELinux: initialized (dev ramfs, type ramfs), uses genfs_contexts > NET: Registered protocol family 10 > lo: Disabled Privacy Extensions > IPv6 over IPv4 tunneling driver > ACPI: Power Button (FF) [PWRF] > ACPI: Power Button (CM) [PWRB] > md: Autodetecting RAID arrays. > md: autorun ... > md: ... autorun DONE. > device-mapper: multipath: version 1.0.5 loaded > EXT3 FS on dm-0, internal journal > kjournald starting. Commit interval 5 seconds > EXT3 FS on dm-1, internal journal > EXT3-fs: mounted filesystem with ordered data mode. > SELinux: initialized (dev dm-1, type ext3), uses xattr > kjournald starting. Commit interval 5 seconds > EXT3 FS on hda1, internal journal > EXT3-fs: mounted filesystem with ordered data mode. > SELinux: initialized (dev hda1, type ext3), uses xattr > SELinux: initialized (dev tmpfs, type tmpfs), uses transition SIDs > Adding 2031608k swap on /dev/VolGroup00/LogVol02. Priority:-1 > extents:1 across:2031608k > SELinux: initialized (dev binfmt_misc, type binfmt_misc), uses > genfs_contexts > IA-32 Microcode Update Driver: v1.14a <tigran@veritas.com> > microcode: CPU2 updated from revision 0x14 to 0x29, date = 08112004 > microcode: CPU1 updated from revision 0x14 to 0x29, date = 08112004 > microcode: CPU3 updated from revision 0x14 to 0x29, date = 08112004 > microcode: CPU0 updated from revision 0x14 to 0x29, date = 08112004 > ip6_tables: (C) 2000-2006 Netfilter Core Team > ip_tables: (C) 2000-2006 Netfilter Core Team > Netfilter messages via NETLINK v0.30. > ip_conntrack version 2.4 (8187 buckets, 65496 max) - 228 bytes per > conntrack > ADDRCONF(NETDEV_UP): eth0: link is not ready > e100: eth0: e100_watchdog: link up, 100Mbps, full-duplex > ADDRCONF(NETDEV_CHANGE): eth0: link becomes ready > libafs: module license 'http://www.openafs.org/dl/license10.html' > taints kernel. > Found system call table at 0xc06154e0 (pattern scan) > Address 0xc06154e0 is not writable. > System call hooks will not be installed; proceeding anyway > enabling dynamically allocated vcaches > Starting AFS cache scan...found 677 non-empty cache files (8%). > SELinux: initialized (dev afs, type afs), uses genfs_contexts > eth0: no IPv6 routers present > SELinux: initialized (dev rpc_pipefs, type rpc_pipefs), uses > genfs_contexts > Bluetooth: Core ver 2.10 > NET: Registered protocol family 31 > Bluetooth: HCI device and connection manager initialized > Bluetooth: HCI socket layer initialized > Bluetooth: L2CAP ver 2.8 > Bluetooth: L2CAP socket layer initialized > Bluetooth: RFCOMM socket layer initialized > Bluetooth: RFCOMM TTY layer initialized > Bluetooth: RFCOMM ver 1.8 > Bluetooth: HIDP (Human Interface Emulation) ver 1.1 > SELinux: initialized (dev autofs, type autofs), uses genfs_contexts > SELinux: initialized (dev autofs, type autofs), uses genfs_contexts > SELinux: initialized (dev autofs, type autofs), uses genfs_contexts > hdd: No disk in drive > > > > 2009/8/10 Pedro Paulo de Magalhães Oliveira Junior > <ppj@netfilter.com.br> > Can you post the output of dmesg command > > > ----------------------------------------------------------- > Pedro Paulo de M. Oliveira Junior > Diretor de Operações > Netfilter & SpeedComm Telecom > --- Novo Netfilter 3.0 www.Netfilter.com.br > --- Em breve Netfilter Small Business > > > > 2009/8/10 corinna bauer <corinnab83@gmail.com> > That didn't work. > > > Corinna > > 2009/8/10 Pedro Paulo de Magalhães Oliveira Junior > <ppj@netfilter.com.br> > > > try: > > > setenv doublebufferflag 1 > > > before running tksurfer > ----------------------------------------------------------- > Pedro Paulo de M. Oliveira Junior > Diretor de Operações > Netfilter & SpeedComm Telecom > --- Novo Netfilter 3.0 www.Netfilter.com.br > --- Em breve Netfilter Small Business > > > > 2009/8/10 corinna bauer <corinnab83@gmail.com> > > When I run tksurfer, only portions of > the cuneus, lateral occipital, and > superior parietal regions are > displayed. This occurs in both FS > versions 4.2.0 and 4.4.0. I am using a > 32 bit BU Linux system which is > equivalent to redhat 5.0. > The error message is similar to those > in previous posts, but previous > suggestions don't seem to help. > > surfer: current subjects > dir: /home/freesurfer4.2.0/subjects/corinna/PET > surfer: not in "scripts" dir ==> using > cwd for session root > surfer: session root data dir > ($session) set to: > surfer: /home/freesurfer4.2.0/subjects/corinna/PET > surfer: Reading header info > from /home/freesurfer4.2.0/subjects/corinna/PET/003_S_1059/mri/T1.mgz > surfer: vertices=119899, faces=239794 > Loading /home/freesurfer4.2.0/surface_labels.txt > surfer: ### redraw failed: no gl > window open > surfer: single buffered window > surfer: tkoInitWindow(003_S_1059) > surfer: using > interface /home/freesurfer4.2.0/lib/tcl/tksurfer.tcl > Reading /home/freesurfer4.2.0/lib/tcl/tkm_common.tcl > Reading /home/freesurfer4.2.0/lib/tcl/tkm_wrappers.tcl > Reading /home/freesurfer4.2.0/lib/tcl/fsgdfPlot.tcl > Reading /home/freesurfer4.2.0/lib/tcl/tkUtils.tcl > Successfully parsed tksurfer.tcl > reading white matter vertex > locations... > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
corinna bauer -
Nick Schmansky -
Pedro Paulo de Magalhães Oliveira Junior