Freesurfer May 2008

freesurfer@nmr.mgh.harvard.edu

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Whole brain GM volume
by deepa preeti 31 May '08

31 May '08

How would I calculate whole brain GM volume in Freesurfer? Any suggestions greatly appreciated. Deepa Ramasamy.

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RE: [Freesurfer] tksurfer display broken: fixed
by Nick Schmansky 30 May '08

30 May '08

Jenifer, I see you have this in your /etc/X11/xorg.conf file: Section "Module" Load "glx" EndSection Others having the recent tksurfer problem should make sure they have these lines as well, as tksurfer uses glx. Also, fyi, you can get a higher display resolution than the default. Try changing this line: Modes "1024x768" "800x600" "640x480" to something like this: Modes "1600x1200" "1280x1024" "1024x768" "800x600" "640x480" It will use the first mode in the list, and if that doesnt work, it will try the next one. You can delete ones that dont work. In other words, put your desired resolution first in the list. Nick On Fri, 2008-05-30 at 13:37 -0500, Juranek, Jenifer wrote: > Hi Nick, > I've attached the current /etc/X11/xorg.conf as a text file. > > Let me know if I can provide any additional info > > Cheers, > Jenifer > > -----Original Message----- > From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] > Sent: Fri 5/30/2008 1:31 PM > To: Juranek, Jenifer > Cc: Freesurfer Mailing List > Subject: Re: [Freesurfer] tksurfer display broken: fixed > > Jenifer, > > Thanks for the detailed info! Just to be clear, does your > current /etc/X11/xorg.conf have the line: > > Load "glx" > > > glx is OpenGL on X-Windows, allowing X windows apps, like tksurfer, to > run using OpenGL, for accelerated graphics. Ideally, you want to load > glx. > > Nick > > > On Fri, 2008-05-30 at 12:42 -0500, Juranek, Jenifer wrote: > > Not exactly sure how or what happened...but did manage to "fix" my tksurfer display problem. > > Since others on the list had reported similar problems, I thought I'd post what I did to "fix" the problem. Since I'm not a Linux guru, my "fix" is probably just a "bandaid"...but it did work...and hopefully the info provides some assistance to others. > > > > Just to note the following particulars of my system: > > RHEL5 (DELL Precision 690n box went live April 16, 2008) > > Linux_x86_64 architecture > > > > 2 kernels: > > drwxr-xr-x 18 root root 4096 May 9 13:50 2.6.18-53.1.19.el5-x86_64 > > drwxr-xr-x 18 root root 4096 May 27 15:02 2.6.18-92.el5-x86_64 > > > > NVIDIA Quadro Fx 3450/4000 SDI > > Driver Version 1.0-9746 > > > > "Friendly" software also installed on the same box=fslv404 > > MATLAB r2008a is also installed (currently running -lgi on bert...I'll update on the outcome of this "friendliness" test) > > > > > > As of yesterday, had several possible scenarios outlined: > > 1) rpm -e dell-nvidia-rhel5-169.12-1dkms.x86_64.rpm > > rpm -ivh dell-nvidia-9746-7dkms.x86_64.rpm > > --> should return to a well-behaved (albeit "older") nvidia > > driver...same as "out of the box" > > > > 2) restore original "out of the box" settings for entire system via > > /usr/var/dell/reinstall.sh > > --> should return ALL system settings to original "out of the box"...good for freesurfer and fsl apps but not so good for matlab... > > > > 3) boot into older kernel (I apparently have a total of 2 listed in > > /usr/src/kernels) > > [root@localhost kernels]# ls -l > > total 16 > > drwxr-xr-x 18 root root 4096 May 9 13:50 2.6.18-53.1.19.el5-x86_64 > > drwxr-xr-x 18 root root 4096 May 27 15:02 2.6.18-92.el5-x86_64 > > > > I attempted (1) first. However, the driver was not well-behaved for bert (tkmedit or tksurfer). > > I attempted (3) second. However, no change in behavior. > > While tarballing to prepare for (3)...since everything worked perfectly fine right out of the box -- before Matlab and before any package updates...I found my *original* /etc/X11/xorg.conf file (from April 16) and cp it into /etc/X11/xorg.conf & rebooted. > > > > RESULTS: > > Was *very* happy to see tksurfer & tkmedit behave properly for bert. > > Proper behavior for tksurfer & tkmedit was observed in both kernels (after the xorg.conf file replacement). > > Still waiting to see if matlab behaves for bert's -lgi. > > > > I diff'd the "original" xorg.conf with the "broken" one and the following lines were returned: > > > > Hope this helps others find their "bandaid" solution to get them up and running again. > > Cheers, > > Jenifer > > > > [root@localhost X11]# diff xorg.conf.backup.OLD xorg.conf.backup > > 1,4c1,2 > > < > > < # nvidia-xconfig: X configuration file generated by nvidia-xconfig > > < # nvidia-xconfig: version 1.0 (buildmeister@builder26) Fri Dec 15 10:40:27 PST 2006 > > < # Xorg configuration created by system-config-display > > --- > > > # nvidia-settings: X configuration file generated by nvidia-settings > > > # nvidia-settings: version 1.0 (buildmeister@builder26) Fri Dec 15 10:40:57 PST 2006 > > 7,10c5,8 > > < Identifier "Default Layout" > > < Screen 0 "Screen0" 0 0 > > < InputDevice "Mouse0" "CorePointer" > > < InputDevice "Keyboard0" "CoreKeyboard" > > --- > > > Identifier "Layout0" > > > Screen 0 "Screen0" 0 0 > > > InputDevice "Keyboard0" "CoreKeyboard" > > > InputDevice "Mouse0" "CorePointer" > > > 13a12,13 > > > RgbPath "/usr/lib64/X11/rgb" > > > FontPath "unix/:7100" > > 17c17,21 > > < Load "glx" > > --- > > > Load "dbe" > > > Load "extmod" > > > Load "type1" > > > Load "freetype" > > > Load "glx" > > 21c25 > > < Option "AllowMouseOpenFail" "yes" > > --- > > > Option "Xinerama" "0" > > 25d28 > > < > > 27,32c30,35 > > < Identifier "Mouse0" > > < Driver "mouse" > > < Option "Protocol" "auto" > > < Option "Device" "/dev/input/mice" > > < Option "Emulate3Buttons" "no" > > < Option "ZAxisMapping" "4 5" > > --- > > > Identifier "Mouse0" > > > Driver "mouse" > > > Option "Protocol" "auto" > > > Option "Device" "/dev/input/mice" > > > Option "Emulate3Buttons" "no" > > > Option "ZAxisMapping" "4 5" > > 36,39c39,43 > > < Identifier "Keyboard0" > > < Driver "kbd" > > < Option "XkbModel" "pc105" > > < Option "XkbLayout" "us" > > --- > > > # generated from data in "/etc/sysconfig/keyboard" > > > Identifier "Keyboard0" > > > Driver "kbd" > > > Option "XkbLayout" "us" > > > Option "XkbModel" "pc105" > > 43,49c47,53 > > < Identifier "Monitor0" > > < VendorName "Unknown" > > < ModelName "Unknown" > > < ### Comment all HorizSync and VertSync values to use DDC: > > < HorizSync 30.0 - 110.0 > > < VertRefresh 50.0 - 150.0 > > < Option "DPMS" > > --- > > > # HorizSync source: edid, VertRefresh source: edid > > > Identifier "Monitor0" > > > VendorName "Unknown" > > > ModelName "DELL 2007WFP" > > > HorizSync 30.0 - 83.0 > > > VertRefresh 56.0 - 76.0 > > > Option "DPMS" > > 53,55c57,60 > > < Identifier "Videocard0" > > < Driver "nvidia" > > < BoardName "NVIDIA PCI-Express Quadro FX 3450" > > --- > > > Identifier "Videocard0" > > > Driver "nvidia" > > > VendorName "NVIDIA Corporation" > > > BoardName "Quadro FX 3450/4000 SDI" > > 59,71c64,72 > > < Identifier "Screen0" > > < Device "Videocard0" > > < Monitor "Monitor0" > > < DefaultDepth 16 > > < SubSection "Display" > > < Viewport 0 0 > > < Depth 24 > > < EndSubSection > > < SubSection "Display" > > < Viewport 0 0 > > < Depth 16 > > < Modes "1024x768" "800x600" "640x480" > > < EndSubSection > > --- > > > Identifier "Screen0" > > > Device "Videocard0" > > > Monitor "Monitor0" > > > DefaultDepth 16 > > > Option "metamodes" "1024x768 +0+0; 1600x1024 +0+0; 800x600 +0+0; 640x480 +0+0; 1280x1024 +0+0" > > > SubSection "Display" > > > Depth 16 > > > Modes "1600x1200" "1280x1024" "1024x768" "800x600" "640x480" > > > EndSubSection > > [root@localhost X11]# > > > > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > >

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tksurfer display broken: fixed
by Juranek, Jenifer 30 May '08

30 May '08

Not exactly sure how or what happened...but did manage to "fix" my tksurfer display problem. Since others on the list had reported similar problems, I thought I'd post what I did to "fix" the problem. Since I'm not a Linux guru, my "fix" is probably just a "bandaid"...but it did work...and hopefully the info provides some assistance to others. Just to note the following particulars of my system: RHEL5 (DELL Precision 690n box went live April 16, 2008) Linux_x86_64 architecture 2 kernels: drwxr-xr-x 18 root root 4096 May 9 13:50 2.6.18-53.1.19.el5-x86_64 drwxr-xr-x 18 root root 4096 May 27 15:02 2.6.18-92.el5-x86_64 NVIDIA Quadro Fx 3450/4000 SDI Driver Version 1.0-9746 "Friendly" software also installed on the same box=fslv404 MATLAB r2008a is also installed (currently running -lgi on bert...I'll update on the outcome of this "friendliness" test) As of yesterday, had several possible scenarios outlined: 1) rpm -e dell-nvidia-rhel5-169.12-1dkms.x86_64.rpm rpm -ivh dell-nvidia-9746-7dkms.x86_64.rpm --> should return to a well-behaved (albeit "older") nvidia driver...same as "out of the box" 2) restore original "out of the box" settings for entire system via /usr/var/dell/reinstall.sh --> should return ALL system settings to original "out of the box"...good for freesurfer and fsl apps but not so good for matlab... 3) boot into older kernel (I apparently have a total of 2 listed in /usr/src/kernels) [root@localhost kernels]# ls -l total 16 drwxr-xr-x 18 root root 4096 May 9 13:50 2.6.18-53.1.19.el5-x86_64 drwxr-xr-x 18 root root 4096 May 27 15:02 2.6.18-92.el5-x86_64 I attempted (1) first. However, the driver was not well-behaved for bert (tkmedit or tksurfer). I attempted (3) second. However, no change in behavior. While tarballing to prepare for (3)...since everything worked perfectly fine right out of the box -- before Matlab and before any package updates...I found my *original* /etc/X11/xorg.conf file (from April 16) and cp it into /etc/X11/xorg.conf & rebooted. RESULTS: Was *very* happy to see tksurfer & tkmedit behave properly for bert. Proper behavior for tksurfer & tkmedit was observed in both kernels (after the xorg.conf file replacement). Still waiting to see if matlab behaves for bert's -lgi. I diff'd the "original" xorg.conf with the "broken" one and the following lines were returned: Hope this helps others find their "bandaid" solution to get them up and running again. Cheers, Jenifer [root@localhost X11]# diff xorg.conf.backup.OLD xorg.conf.backup 1,4c1,2 < < # nvidia-xconfig: X configuration file generated by nvidia-xconfig < # nvidia-xconfig: version 1.0 (buildmeister@builder26) Fri Dec 15 10:40:27 PST 2006 < # Xorg configuration created by system-config-display --- > # nvidia-settings: X configuration file generated by nvidia-settings > # nvidia-settings: version 1.0 (buildmeister@builder26) Fri Dec 15 10:40:57 PST 2006 7,10c5,8 < Identifier "Default Layout" < Screen 0 "Screen0" 0 0 < InputDevice "Mouse0" "CorePointer" < InputDevice "Keyboard0" "CoreKeyboard" --- > Identifier "Layout0" > Screen 0 "Screen0" 0 0 > InputDevice "Keyboard0" "CoreKeyboard" > InputDevice "Mouse0" "CorePointer" 13a12,13 > RgbPath "/usr/lib64/X11/rgb" > FontPath "unix/:7100" 17c17,21 < Load "glx" --- > Load "dbe" > Load "extmod" > Load "type1" > Load "freetype" > Load "glx" 21c25 < Option "AllowMouseOpenFail" "yes" --- > Option "Xinerama" "0" 25d28 < 27,32c30,35 < Identifier "Mouse0" < Driver "mouse" < Option "Protocol" "auto" < Option "Device" "/dev/input/mice" < Option "Emulate3Buttons" "no" < Option "ZAxisMapping" "4 5" --- > Identifier "Mouse0" > Driver "mouse" > Option "Protocol" "auto" > Option "Device" "/dev/input/mice" > Option "Emulate3Buttons" "no" > Option "ZAxisMapping" "4 5" 36,39c39,43 < Identifier "Keyboard0" < Driver "kbd" < Option "XkbModel" "pc105" < Option "XkbLayout" "us" --- > # generated from data in "/etc/sysconfig/keyboard" > Identifier "Keyboard0" > Driver "kbd" > Option "XkbLayout" "us" > Option "XkbModel" "pc105" 43,49c47,53 < Identifier "Monitor0" < VendorName "Unknown" < ModelName "Unknown" < ### Comment all HorizSync and VertSync values to use DDC: < HorizSync 30.0 - 110.0 < VertRefresh 50.0 - 150.0 < Option "DPMS" --- > # HorizSync source: edid, VertRefresh source: edid > Identifier "Monitor0" > VendorName "Unknown" > ModelName "DELL 2007WFP" > HorizSync 30.0 - 83.0 > VertRefresh 56.0 - 76.0 > Option "DPMS" 53,55c57,60 < Identifier "Videocard0" < Driver "nvidia" < BoardName "NVIDIA PCI-Express Quadro FX 3450" --- > Identifier "Videocard0" > Driver "nvidia" > VendorName "NVIDIA Corporation" > BoardName "Quadro FX 3450/4000 SDI" 59,71c64,72 < Identifier "Screen0" < Device "Videocard0" < Monitor "Monitor0" < DefaultDepth 16 < SubSection "Display" < Viewport 0 0 < Depth 24 < EndSubSection < SubSection "Display" < Viewport 0 0 < Depth 16 < Modes "1024x768" "800x600" "640x480" < EndSubSection --- > Identifier "Screen0" > Device "Videocard0" > Monitor "Monitor0" > DefaultDepth 16 > Option "metamodes" "1024x768 +0+0; 1600x1024 +0+0; 800x600 +0+0; 640x480 +0+0; 1280x1024 +0+0" > SubSection "Display" > Depth 16 > Modes "1600x1200" "1280x1024" "1024x768" "800x600" "640x480" > EndSubSection [root@localhost X11]#

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SELinux AVC denial: Matlab
by Juranek, Jenifer 30 May '08

30 May '08

While trying to check if -lgi will run on bert (on RHEL5,fsv404 and matlab r2008a), I received the following message from SELinux (please see summary below): Sorry to be so cautious, but do I change to allow_execheap boolean? The system-wide impact statement makes me a little nervous... Many thanks for any advice you can provide, Jenifer Summary: SELinux is preventing MATLAB from changing the access protection of memory on the heap. Detailed Description: [SELinux is in permissive mode, the operation would have been denied but was permitted due to permissive mode.] The MATLAB application attempted to change the access protection of memory on the heap (e.g., allocated using malloc). This is a potential security problem. Applications should not be doing this. Applications are sometimes coded incorrectly and request this permission. The SELinux Memory Protection Tests (http://people.redhat.com/drepper/selinux-mem.html) web page explains how to remove this requirement. If MATLAB does not work and you need it to work, you can configure SELinux temporarily to allow this access until the application is fixed. Please file a bug report (http://bugzilla.redhat.com/bugzilla/enter_bug.cgi) against this package. Allowing Access: If you want MATLAB to continue, you must turn on the allow_execheap boolean. Note: This boolean will affect all applications on the system. The following command will allow this access: setsebool -P allow_execheap=1 Additional Information: Source Context root:system_r:unconfined_t:SystemLow-SystemHigh Target Context root:system_r:unconfined_t:SystemLow-SystemHigh Target Objects None [ process ] Source MATLAB Source Path /usr/local/MATLAB_R2008a/bin/glnxa64/MATLAB Port <Unknown> Host localhost.localdomain Source RPM Packages Target RPM Packages Policy RPM selinux-policy-2.4.6-137.el5 Selinux Enabled True Policy Type targeted MLS Enabled True Enforcing Mode Permissive Plugin Name allow_execheap Host Name localhost.localdomain Platform Linux localhost.localdomain 2.6.18-92.el5 #1 SMP Tue Apr 29 13:16:15 EDT 2008 x86_64 x86_64 Alert Count 1 First Seen Thu 29 May 2008 01:55:19 PM CDT Last Seen Thu 29 May 2008 01:55:19 PM CDT Local ID 547d8303-5b60-4883-adc1-5da588da0b2a Line Numbers Raw Audit Messages host=localhost.localdomain type=AVC msg=audit(1212087319.314:56): avc: denied { execheap } for pid=9538 comm="MATLAB" scontext=root:system_r:unconfined_t:s0-s0:c0.c1023 tcontext=root:system_r:unconfined_t:s0-s0:c0.c1023 tclass=process host=localhost.localdomain type=SYSCALL msg=audit(1212087319.314:56): arch=c000003e syscall=10 success=yes exit=0 a0=68d4000 a1=553 a2=7 a3=3 items=0 ppid=9460 pid=9538 auid=0 uid=500 gid=500 euid=500 suid=500 fsuid=500 egid=500 sgid=500 fsgid=500 tty=pts5 ses=1 comm="MATLAB" exe="/usr/local/MATLAB_R2008a/bin/glnxa64/MATLAB" subj=root:system_r:unconfined_t:s0-s0:c0.c1023 key=(null)

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ERROR: cannot find .../mri/aseg.auto_noCCseg.mgz
by Sky Raptentsetsang 30 May '08

30 May '08

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Autorecon1 and combining data from different sessions
by Damian Jenkins 30 May '08

30 May '08

I have two sets of images, one collected at timepoint 1 and one at timepoint 2, for each patient and control in an MS study. I am now trying to run autorecon1 on this data, at the same time attempting to form a combined model fit. I am using the following script: for subject in ***; do if [ ! -f $SUBJECTS_DIR/$subject-1/mri/brainmask.mgz ]; then fsl_sub -q short.q -a lx24-amd64 -l ../group_study/logs recon-all -i $subject/00/struct_noneck.nii.gz -i $subject/02/struct_noneck.nii.gz -subjid $subject-1 -autorecon1 -force The following error message is generated for the around half of the subjects, yet there seems to be nothing especially different between the ones that work and the ones that fail. error reading from file /Volumes/Data/magnims/group_study/P21-1/mri/tmp-mri_motion_correct.fsl-8454/cor-2.img mri_average: MRIread(/Volumes/Data/magnims/group_study/P21-1/mri/tmp-mri_motion_correct.fsl-8454/cor-2.img) failed Any ideas? Thanks, Damian Dr Damian Jenkins Department of Clinical Neurology Oxford University

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tksurfer not working
by Dr. Glenn Lawyer 30 May '08

30 May '08

Hi, In my first post on this I said Matlab was not installed on my machine. I was wrong; matlab had been installed. +glenn

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libexpat.so.1 error
by Deane Aikins 29 May '08

29 May '08

I'm installing v4.0.4 on a CentOS 4.1 i686 computer. When I go to run tkmedit, I get an error regarding libexpat.so.1. Do I need a file that is specifically for the i686 or will a lobexpat.so.1 for i586 work? Thanks, Deane

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tksurfer display broken: post re-install nvidia 9746
by Juranek, Jenifer 29 May '08

29 May '08

I re-installed the dell-nvidia driver (original with system). Some new behavior observed with bert: tksurfer bert lh pial yields a complete "bert" window (entire pial surface is displayed). However, the lower window "TkSurfer Tools" is not visible. Also, tkmedit bert norm.mgz fails to launch a display, simply returns a command prompt. I've pasted the screen output for tksurfer below: Any ideas are greatly appreciated. [jjuranek@localhost subjects]$ tksurfer bert lh pial surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /usr/local/freesurfer/subjects surfer: Reading header info from /usr/local/freesurfer/subjects/bert/mri/T1.mgz surfer: vertices=131168, faces=262332 Loading /usr/local/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(bert) Tk_Init failed: this isn't a Tk applicationunknown color name "Black" Tix_Init failed: this isn't a Tk applicationunknown color name "Black" surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Error sourcing /usr/local/freesurfer/lib/tcl/tksurfer.tcl: this isn't a Tk applicationunknown color name "Black" surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_InflatedVSetLoaded 0: can't read "glEnableGroups(mg_InflatedVSetLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_PialVSetLoaded 0: can't read "glEnableGroups(mg_PialVSetLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_TimeCourseLoaded 0: can't read "glEnableGroups(mg_TimeCourseLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_OverlayLoaded 0: can't read "glEnableGroups(mg_OverlayLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_CurvatureLoaded 0: can't read "glEnableGroups(mg_CurvatureLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_LabelLoaded 0: can't read "glEnableGroups(mg_LabelLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_FieldSignLoaded 0: can't read "glEnableGroups(mg_FieldSignLoaded)": no such variable surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_FieldMaskLoaded 0: can't read "glEnableGroups(mg_FieldMaskLoaded)": no such variable surfer: Error sending tcl command UpdateUndoItemLabel "Nothing to Undo": invalid command name "UpdateUndoItemLabel" surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_OriginalVSetLoaded 1: can't read "glEnableGroups(mg_OriginalVSetLoaded)": no such variable surfer: Error sending tcl command LblLst_SetStructures { 0 Unknown 1 G_cingularis 2 G_cuneus 3 G_frontalis_inf-pars_opercularis 4 G_frontalis_inf-pars_orbitalis 5 G_frontalis_inf-pars_triangularis 6 G_frontalis_medius 7 G_frontalis_sup-pars_lateralis 8 G_frontalis_sup-pars_medialis 9 G_frontomarginalis 10 G_hippocampi 11 G_insularis_breves 12 G_occipitalis_inf 13 G_occipitalis_medius-pars_inf 14 G_occipitalis_medius-pars_sup 15 G_occipitalis_sup 16 G_lateralis 17 G_lingualis 18 G_parahippocampi 19 G_orbitalis 20 G_paracentralis 21 G_parietalis_inf-pars_angularis 22 G_parietalis_inf-pars_supramarginalis 23 G_parietalis_sup 24 G_postcentralis 25 G_precentralis 26 G_precuneus 27 G_rectus_and_S_orbitalis_medialis 28 G_rectus_and_S_orbitalis_medialis2 29 G_subcentralis 30 G_supracingularis 31 G_temporalis_transversalis 32 G_temporalis_inf 33 G_temporalis_medius 34 G_temporalis_sup-pars_lateralis 35 G_temporalis_sup-planum_polare 36 G_temporalis_sup-planum_temporale 37 Plica_falciformis 38 Polus_occipitalis 39 Polus_temporalis 40 S_temporalis_transversalis 42 S_angularis 43 S_calcarinus 44 S_centralis_insulae_&_G_insularis_longus 46 S_centralis 47 S_cingularis 48 S_cingularis-pars_marginalis 49 S_circularis_insulae_ant 50 S_circularis_insulae_inf 51 S_circularis_insulae_sup 52 S_corpori_callosi 53 S_diagonalis 54 S_frontalis_inf 55 S_frontalis_medialis 56 S_frontalis_medius 57 S_frontalis_sup 58 S_frontomarginalis 59 S_intermedius_primus 60 S_intermedius_secundus 61 S_intracingularis 62 S_intraoccipitalis_medius 63 S_intraoccipitotemporalis_lateralis 64 S_intraparietalis 65 S_lateralis-pars_ant-ramus_horizontalis 66 S_lateralis-pars_ant-ramus_verticalis 67 S_lateralis-pars_horizontalis 68 S_lateralis-pars_post 69 S_lunatus 70 S_occipitalis_ant 71 S_occipitalis_inf 72 S_occipitalis_medius 73 S_occipitalis_sup 74 S_occipitalis_transversalis 75 S_occipitopolaris 76 S_occipitotemporalis_lateralis 77 S_occipitotemporalis_medialis 78 S_orbitales 79 S_orbitalis_lateralis 80 S_paracalcarinus 81 S_paracentralis 82 S_parietalis_transversalis 83 S_parieto_occipitalis 84 S_postcentralis 85 S_precentralis 86 S_retrocalcarinus 87 S_rhinalis 88 S_subcentralis_ant_&_post_ 89 S_suborbitalis 90 S_subparietalis 91 S_supracingularis 92 S_temporalis_inf 93 S_temporalis_sup 94 S_triangularis }: invalid command name "LblLst_SetStructures" reading white matter vertex locations... surfer: Error sending tcl command tkm_SetEnableGroupStatus mg_WhiteVSetLoaded 1: can't read "glEnableGroups(mg_WhiteVSetLoaded)": no such variable surfer: Error sending tcl command UpdateLinkedVarGroup all: invalid command name "UpdateLinkedVarGroup" % surfer: Error sending tcl command MoveToolWindow 663 681: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 664 681: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 666 681: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 667 681: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 669 681: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 671 681: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 675 681: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 675 681: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 683 684: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 691 684: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 703 690: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 705 690: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 713 690: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 727 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 729 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 739 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 740 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 743 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 753 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 756 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 766 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 774 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 790 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 793 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 813 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 813 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 829 696: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 845 696: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 848 696: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 851 696: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 852 696: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 855 696: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 856 695: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 860 695: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 862 695: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 866 695: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 868 695: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 874 695: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 876 695: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 878 695: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 884 695: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 887 695: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 892 695: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 894 695: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 896 695: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 899 695: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 901 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 902 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 905 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 906 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 908 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 910 694: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 911 693: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 916 693: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 917 692: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 919 692: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 922 691: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 923 690: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 926 689: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 927 689: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 928 688: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 931 687: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 932 686: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 933 686: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 934 686: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 934 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 935 685: invalid command name "MoveToolWindow"

1 0

Mac OS & bash-file
by MRI CDPI 29 May '08

29 May '08

Dear Freesurfers, i am a brand new user of a Mac Pro without any experience of that system. I am trying to include in the bash file the startup commands for Freesurfer, but i could find a way to save the changes in the bash file. I already tried to change the permission status of the bashrc file with chmod +w bashrc, but it is not possible, just says "Operation not permitted". Could somebody help me with this? Thanks a lot, Cheers, Thomas

1 0

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Freesurfer May 2008