Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30079 discussions

mgz header dump
by Michael Harms 21 Oct '07

21 Oct '07

I'm sure this is trivial, but I can't find the answer: How do you dump the header contents of an mgz file to the terminal? How about the optional information stored after the image data? thanks, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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Version 4.1 questions
by Kt Labadie 19 Oct '07

19 Oct '07

I have 2 questions related to version 4.1. 1) The ReconAllDevTable on the Martinos Center Freesurfer Wiki is not updated to reflect the new steps in version 4.1. Does anyone have a breakdown of these new steps? I was not sure of the flags for these new steps, or where they fit in (are they part of 2-pial, 2-cp or 3?) Is the wiki going to be updated to reflect this new version? 2) When I load an image in tkmedit (after it has been run all the way through step 3) I get an error message and it won't load the aseg. The aseg is there, I just have to load it manually. Did the following flag change with the new version? brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white - segmentation mri/aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt Thanks. KT LaBadie

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Talairach transformations in tkmedit and tkregister2
by Dr. Claudia Wheeler-Kingshott 17 Oct '07

17 Oct '07

Hi, We have a problem with the Talairach transformations. When we load the talairach.mgz file using tkmedit the axial and coronal orientations are swapped and displaced in the window. The puzzling thing is that if we use tkregister2, the registration is very good. Any idea of why? I found a previous message that had a similar problem but using both the tkmedit and tkregister2. Can we assume that in our case it is all fine, given that tkregister2 seems to be OK? Claudia -- ----------------------------------------- Claudia Wheeler-Kingshott, PhD Senior Lecturer Department of Inflammation Institute of Neurology, UCL Queen Square London WC1N 3BG tel. 0207 8373711 x4301 email: c.wheeler-kingshott(a)ion.ucl.ac.uk

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Interpretation of cortical thickness result
by Martin Kavec 16 Oct '07

16 Oct '07

Hi folks, I have been puzzled for a while with the results from couple of my subjects. They all have clearly visible cerebral atrophy (says neuroradiologist). I ran them through FS-4.0.1 and aseg.stat gives me, as expected, severe loss of gray matter (and others as well) as follows: GM ICV normalized Age matched reference ICV normalized What's puzzling me is the cortical thickness. Except of few locations, cortical thickness is within the STD of the controls, and at places it's even thicker. I am wondering, where such a huge GM volume loss (aseg.stats) comes from? Very simplified explanation could be that there is ^3 relation between volume and one of the dimensions of a structure ( V ~ x^3 ). In that case, it would be more sensitive to look at the volume of a parcelated cortical GM. But then, the intersubject variability of the cortical area would come into the play. Is there any other explanation? Is there a single parameter assessing cortical atrophy? Thanks a lot for the ideas in advance . Martin PS.: BTW, what is happening with the OASIS dataset analyzed using FS? When it was released the first time, there were some inconsistencies and it was pulled down from the ftp.

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Problems with make_average_subject
by jorge luis 16 Oct '07

16 Oct '07

Hello all I am trying to build an average subject under FS X86-64 v4.0.1 and I get the follow: [root@localhost ~]$ make_average_subject --subjects subj1 subj10 subj11 --out subjavr limit: descriptors: No se puede %s: %s: No se puede %s el lÃmite %s el lÃmite [root@localhost ~]$ The words in spanish should came from the operating system. Any idea? In advance thank you ____________________________________________________________________________________ Sé un Mejor Amante del Cine ¿Quieres saber cómo? ¡Deja que otras personas te ayuden! http://advision.webevents.yahoo.com/reto/entretenimiento.html

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[Fwd: optimal reconstruction.]
by Nick Schmansky 15 Oct '07

15 Oct '07

Shrikanth, I am re-posting this question to the freesurfer list, as others may have a better answer. To the best of my knowledge, there is no single error measure for which a comparison can be made of the quality of a surface reconstruction across subjects. Rather, a visual inspection of each surface, making use of tksurfer (and tkmedit), will reveal gross defects, and how faithfully it follows the wm/gm boundary. Bruce may have other suggestions. Nick -------- Forwarded Message -------- From: kulashek(a)mappi.helsinki.fi To: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> Subject: optimal reconstruction. Date: Mon, 15 Oct 2007 11:31:40 +0300 Hi, I have recently finished the construction of the inflated surfaces for 10 subjects using Freesurfer. Out of these 10 inflated surfaces how can I find the most accurate(optimal) suface, i.e. the surface with the least amount of error during the reconstruction. Thank you. Regards, Shrikanth

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hyperthreading
by Michael Harms 15 Oct '07

15 Oct '07

Hello, Question about eking out maximum machine performance: Is there a performance advantage (or alternatively penalty) for running twice as many FreeSurfer jobs (simultaneously) as physical CPUs on a Linux machine with HyperThreading enabled CPUs? That is, say you have two physical cores with HyperThreading -- the Linux OS treats this as four logical processors. However, given that Freesurfer is very 'execute' intensive is there any advantage to be gained by running 4 rather than 2 FS jobs simultaneously? Or will the total time per brain with 4 simultaneous jobs be (on average) just twice as long? thanks, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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mincinfo broken pipe
by Chuck Theobald 12 Oct '07

12 Oct '07

Hi, Following some system upgrade to our Linux 2.6 systems, freesurfer has ceased to work. When running recon-all on bert, we get a message referring to a broken pipe and a crash in mincinfo. We are running Gentoo: doolin ~ # uname -a Linux doolin 2.6.21-gentoo-r4 #1 SMP Thu Aug 9 09:33:11 PDT 2007 i686 AMD Athlon(tm) 64 X2 Dual Core Processor 4400+ AuthenticAMD GNU/Linux doolin ~ # Any help and/or advice would be appreciated. Thank you, Chuck mri_add_xform_to_header -c /vxfsvol/home/staff/chuck/freesurfer-test/bert/mri/transforms/talairach.xfm /vxfsvol/home/staff/chuck/freesurfer-test/bert/mri/orig.mgz /vxfsvol/home/staff/chuck/freesurfer-test/bert/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Nu Intensity Correction Fri Oct 12 10:37:03 PDT 2007 mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 /vxfsvol/home/staff/chuck/freesurfer-test/bert/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.3.2.1 2006/11/24 20:16:38 nicks Exp $ Linux doolin 2.6.21-gentoo-r4 #1 SMP Thu Aug 9 09:33:11 PDT 2007 i686 AMD Athlon(tm) 64 X2 Dual Core Processor 4400+ AuthenticAMD GNU/Linux Fri Oct 12 10:37:03 PDT 2007 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 tmpdir is ./tmp.mri_nu_correct.mni.28553 /vxfsvol/home/staff/chuck/freesurfer-test/bert/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.28553/nu0.mnc mri_convert orig.mgz ./tmp.mri_nu_correct.mni.28553/nu0.mnc reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to ./tmp.mri_nu_correct.mni.28553/nu0.mnc... -------------------------------------------------------- Iteration 1 Fri Oct 12 10:37:11 PDT 2007 nu_correct -clobber ./tmp.mri_nu_correct.mni.28553/nu0.mnc ./tmp.mri_nu_correct.mni.28553/nu1.mnc [chuck@doolin:/vxfsvol/home/staff/chuck/freesurfer-test/bert/mri/] [2007-10-12 10:37:11] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_28603/ ./tmp.mri_nu_correct.mni.28553/nu0.mnc ./tmp.mri_nu_correct.mni.28553/nu1.imp nu_estimate_np_and_em: broken pipe nu_estimate_np_and_em: crashed while running mincinfo (termination status=13) nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) ERROR: nu_correct Linux doolin 2.6.21-gentoo-r4 #1 SMP Thu Aug 9 09:33:11 PDT 2007 i686 AMD Athlon(tm) 64 X2 Dual Core Processor 4400+ AuthenticAMD GNU/Linux recon-all exited with ERRORS at Fri Oct 12 10:37:11 PDT 2007 chuck@doolin /usr/local/freesurfer $ -- Chuck Theobald System Administrator The Robert and Beverly Lewis Center for Neuroimaging University of Oregon P: 541-346-0343 F: 541-346-0345

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selxavg3 memory error
by ckeller＠nmr.mgh.harvard.edu 12 Oct '07

12 Oct '07

Hi, I am trying to run an fMRI gamma analysis and am running into memory problems. I'm running freesurfer version stable 4.0 on unix through multnomah. The subject directory is located in /space/multnomah/3/users/gow/PROZ06/MRI/PROZ06004. We're running into issues with the selxavg-sess command. While in the /space/multnomah/3/users/gow/PROZ06/StudyDir I ran selxavg3-sess -sf sessid04 -df sesspar -analysis sm-gamma-fwhm5 -overwrite and got a memory error from matlab. Now this worked one time with using just one run, but when I try to analyze all three runs it returned the error and then when I went back and reran just that one run I received the same error. Below is my code. Thanks. multnomah:jsegawa[91] selxavg3-sess -sf sessid04 -df sesspar -analysis sm-gamma- fwhm5 -overwrite -------------------------------------------------------------- selxavg3-sess logfile is /autofs/space/multnomah_003/users/gow/PROZ06/StudyDir/l og/selxavg3-sess-bold-sm-gamma-fwhm5-071012122828.log -------------------------------------------------------------- ------------------------------------------- /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06004 Fri Oct 12 12:28:28 EDT 2007 anadir = /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06004/bold/sm-gamm a-fwhm5 analysis sm-gamma-fwhm5 alread exists for PROZ06004 ... reanalyzing (deleting old analysis) ------------------------------------------ ------- matlab output -------------------- Warning: Unable to open display iconic, MATLAB is starting without a display. You will not be able to display graphics on the screen. Warning: MATLAB is starting without a display, using internal event queue. You will not be able to display graphics on the screen. < M A T L A B > Copyright 1984-2005 The MathWorks, Inc. Version 7.1.0.183 (R14) Service Pack 3 August 02, 2005 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. Adding MNE Toolbox... >> >> >> >> >> >> >> /usr/local/freesurfer/stable4/fsfast/toolbox/fast_selxavg3. m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> $Id: fast_selxavg3.m,v 1.55.2 .1 2007/09/27 15:25:58 greve Exp $ outtop = /autofs/space/multnomah_003/users/gow/PROZ06/MRI Extension format = nii UseFloat = 0 INFO: acfbins is not set, setting to 10 INFO: mask is not set, setting to brain 1 simple-v-complex.mat Loaded /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06004/bold/010/parfi le1.par as a par2 file. nruns = 1 autostimdur = 1 outanadir = /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06004/bold/sm-g amma-fwhm5 Found 49490/110592 (44.8) voxels in mask Creating Design Matrix Loaded /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06004/bold/010/parfi le1.par as a par2 file. ntptot = 414, nX = 8, DOF = 406 XCond = 288.38 (normalized) Computing compensation for resdual AR1 bias 1 -0.5 -0.501599 (t=0.113866) 2 -0.25 -0.257524 (t=0.220947) 3 0 -0.0157544 (t=0.325266) 4 0.25 0.221692 (t=0.429817) 5 0.5 0.449162 (t=0.537974) AR1 Correction M: 0.0218428 1.0499 Computing contrast matrices Loaded /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06004/bold/010/parfi le1.par as a par2 file. 1 simple-v-complex J= 1 eff = 78.7 vrf = 78.7205 vrfffx = 78.7205 r = 1. 00 OLS Beta Pass run 1 t= 0.0 Loaded /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06004/bold/010/parfi le1.par as a par2 file. Global In-Mask Mean = 544.358 Rescale Target = 100 RescaleFactor = 0.183703 OLS Residual Pass run 1 t= 0.0 Loaded /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06004/bold/010/parfi le1.par as a par2 file. ??? Error using ==> unknown Out of memory. Type HELP MEMORY for your options. Error in ==> fast_selxavg3 at 417 rho1run = sum(rrun(1:end-1,:).*rrun(2:end,:))./rsserun; >> ------------------------------------------ ERROR: fast_selxavg3() failed\n multnomah:jsegawa[92]

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Re: [Analysis-bugs] 4.0.1 bug supposedly fixed with curvature
by Nick Schmansky 12 Oct '07

12 Oct '07

William, Freesurfer v3.0.5 is available for download from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable/cento… Would it be possible for you to create a tarball of that subject and send it to me? I would like to try to recreate the problem here (as I am not able to recreate this problem using my own subject data). To create a tarball: cd $SUBJECTS_DIR tar zcvf subj.tgz subj (where 'subj' is the name of a subject) and then upload to me via the filedrop: https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Nick On Fri, 2007-10-12 at 14:31 -0400, William R Mcgarry wrote: > Hello, > My name is William McGarry and I just submitted a bug report, but failed to include the following: > > FREESURFER_HOME: /usr/local/freesurfer > Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.1 > RedHat release: Fedora Core release 5 (Bordeaux) > Kernel info: Linux 2.6.20-1.2320.fc5 x86_64 > > After updating to v4.0.0, the program would crash after trying to apply curvature mapping with the following output: > reading white matter vertex locations... > % alloc: invalid block: 0xbb7760: 0 0 0 > > Abort > The curvature check box is also checked under "view," so we updated to v4.0.1 which was supposed to fix this problem, yet it persists. This is an x86_64 quad-core Xeon running Fedora Core 5 on the 64bit CentOS tksurfer distribution. Please let us know if you have any information for work arounds, updates, or if you could please provide us with a link to v3.0.5 (the directory "Archive" is a bad link under surfer.nmr.mgh.harvard.edu/pub/dist) Thank you. > Cordially, > William McGarry > _______________________________________________ > Analysis-bugs mailing list > Analysis-bugs(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/analysis-bugs > >

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