Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30081 discussions

(no subject)
by Irene Mattisi 02 Jun '08

02 Jun '08

Hi Bruce! yesterday I asked you if it is possible with the new FS version to obtain the cerebellar cortical volume. You told me that it should be one of the entries in the aseg.stats file (left and right cerebellar cortex). Now I'm not very good with FS, so can you explain me where can I find the entries in the aseg. stats file? Thanks!! Irene Mattisi

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Research Associate Position at School of Psychiatry, UNSW, Australia
by wanlin 01 Jun '08

01 Jun '08

- *Research Associate/ Research Fellow* Faculty of Medicine SCHOOL OF PSYCHIATRY University of New South Wales *REF. 5871NET* Fixed Term: The Salary range: Research Associate A$51K - A$68K per year; Research Fellow A$71K- A$84K per year depending on qualifications and experience ( plus up to 17% employer superannuation and leave loading) Applicants from suitably qualified backgrounds are invited to apply for the role of a Research Associate/Research in the area of brain functional Magnetic Resonance Imaging (fMRI) within the School of Psychiatry and Brain Sciences UNSW. The position is offered as part of the /Brain and Ageing Program/, a high profile research program funded by the National Health and Medical Research Council (NHMRC), which aims to evaluate the determinants of age related cognitive disorders. The Program comprises a number of large studies with an opportunity to participate in other studies and/or initiate new projects. The position is currently based at the Neuropsychiatric Institute in Randwick. It provides an opportunity to work with a diligent and dedicated team of local and international researchers, and an avenue for a research career in the field of functional neuroimaging. The position is a key role within the program. The successful applicant will be required to develop new 'leading edge' research projects and will have the primary responsibility for the preparation of research applications for funding from national and international resources. They will be responsible for the implementation and completion of various fMRI studies in neuropsychiatry, along with providing leadership and training to junior researchers in performing functional MRI studies. The successful applicant will have completed, be nearing the completion of, a PhD in a relevant discipline, and have experience in the use of fMRI to study cognitive/clinical function. The successful applicant will also have been published in neuroimaging journals and have presented at related conferences. Knowledge and experience of multi-modal functional neuroimaging will be highly regarded. Applications are encouraged from a variety of backgrounds, including neuroscience, medicine, psychology, engineering, mathematics and computer science. This position is a full time, fixed term appointment for 12 months with the possibility of renewal for the life of the Program. The successful applicant may be required to undertake a criminal record check. Applicants should systematically address the selection criteria in their application. *Having read all the documentation you may then direct any enquiries to* *Dr Wei Wen (applicants from mathematics, computer science, engineering or related backgrounds) on (61 2) 9382 3730 or w.wen(a)unsw.edu.au <mailto:w.wen@unsw.edu.au> or Professor Perminder Sachdev (applicants from psychology, medicine or other clinical backgrounds) on (61 2) 9382 3763 or p.sachdev(a)unsw.edu.au <mailto:p.sachdev@unsw.edu.au> *For an Information pack, click HERE <http://www.hr.unsw.edu.au/services/recruitment/jobs/info/pd16050806.pdf> *Applications close : 04 June 2008*

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(no subject)
by Irene Mattisi 01 Jun '08

01 Jun '08

Hi everybody, I would like to know if with the new version of FS I can also obtain the cerebellar cortical volume. Thanks Irene Mattisi Multiple Sclerosis Centre of Padua, Italy

2 1

Whole brain GM volume
by deepa preeti 31 May '08

31 May '08

If I need whole brain Gray matter (GM) volume, can I add just left GM and Right GM volumes after runing mris_anatomical_stats on ?h.cortex.label (in the label directory). I appreciate your suggestions. Thanks, Deepa Ramasamy.

2 1

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 > > > > > > >

2 1

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]#

2 1

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

3 7

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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