Freesurfer October 2007

freesurfer@nmr.mgh.harvard.edu

55 participants
79 discussions

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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how/where is talairach.xfm used?
by Michael Harms 12 Oct '07

12 Oct '07

Hello, We are running FS v3.0.5 on some elderly brains, and the talairach transform (as assessed via tkregister2 with fstal flag) is inaccurate in an appreciable number of the scans we have examined so far. Frequently, the inaccuracies involve primarily scaling or translation, although in one instance the rotation was way-off (such that the cardinal axes were basically swapped). However, even for this worst case, the white and pial surfaces, as well as the aseg, look reasonable. (I haven't run autorecon3 to create the surface parcellations yet). To what extent is talairach.xfm important for the autorecon2 & 3 stages? If surfaces and aseg look ok, can an inaccurate talairach.xfm just be ignored if we are not going to be averaging functional data? Will the surface parcellations perhaps be affected somehow? Looking at ReconAllDevTable it appears that talairach.lta and talairach.m3z are the primary inputs to stages 2 and 3. So, I'm wondering how the .xfm relates to the .lta and .m3z files...? Lastly, the particularly bad .xfm under v3.0.5 looks fine when created using v4.0.1. If we need or want accurate .xfm's would it be appropriate to run autorecon1 under v4 but then switch to v3 for autorecon2 & 3 so as to maintain compatibility with other subjects processed under v3? 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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problem with dt_recon
by Dirk Dettmering 11 Oct '07

11 Oct '07

Hello, after I figured out how to prepare the dt_recon command with the correct input (which was a long struggle to find the correct dicom input) I got now stuck as dt_recon always stops before finishing the run with the same error message: brainmask not found I attach the log file with the relevant parts. The complete log and subject dir is available upon request. Does somebody know whats wrong? I created the complete directory tree under the subjects dir with mksubjdirs. The dicom input was created with unpacksdcmdir -src 02171336/ -targ mri -run 2 dicom dicom 002 after I copied the content of the dicom data directory from cd to disk. And thats exactly the stage where I was stuck a long time as it wasn't obvious to me to prepare dicom data with unpacksdcmdir to dicom format to satisfy dt_recon. Thanks for any hint or help in advance Dirk -- Dirk Dettmering DV-Koordinator - Klinik für Neurologie Universitätsklinikum Gießen und Marburg GmbH, Standort Marburg Baldingerstraße D-35043 Marburg Telefon (+49) 06421 - 286 5354 Telefax (+49) 06421 - 286 5208 Pager 142 69684 E-Mail: dirk.dettmering(a)med.uni-marburg.de url: http://www.med.uni-marburg.de Aufsichtsratsvorsitzender: Wolfgang Pföhler Geschäftsführung: Gerald Meder (Vors.), Prof. Dr. Werner Seeger (stv. Vors.), Dr. Hans-Jürgen Hackenberg, Prof. Dr. Martin Hansis, Dr. Peter Mein, Manfred Wiehl Sitz der Gesellschaft: Gießen Amtsgericht Gießen HRB 6384 dt_recon logfile Do Okt 11 18:09:09 CEST 2007 VERSION $Id: dt_recon,v 1.6.2.2 2007/08/23 19:17:46 greve Exp $ setenv SUBJECTS_DIR /mrt-daten/dt_recon/0001_DTI_RLS2 cd /mrt-daten/dt_recon/0001_DTI_RLS2 /usr/local/freesurfer/bin/dt_recon --i mri/dicom/002/29265430 --o maps --s . ixneurol247.med.uni-marburg.de surfer /usr/local/freesurfer/fsl/bin/eddy_correct #@#------------------------------- Converting input Do Okt 11 18:09:09 CEST 2007 cd /mrt-daten/dt_recon/0001_DTI_RLS2 mri_convert /mrt-daten/dt_recon/0001_DTI_RLS2/mri/dicom/002/29265430 /mrt-daten/dt_recon/0001_DTI_RLS2/maps/dwi.nii mri_convert /mrt-daten/dt_recon/0001_DTI_RLS2/mri/dicom/002/29265430 /mrt-daten/dt_recon/0001_DTI_RLS2/maps/dwi.nii $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ reading from /mrt-daten/dt_recon/0001_DTI_RLS2/mri/dicom/002/29265430... Getting Series No INFO: Found 2103 files in /mrt-daten/dt_recon/0001_DTI_RLS2/mri/dicom/002 INFO: Scanning for Series Number 2 Scanning Directory INFO: found 2100 files in series INFO: loading series header info. RunNo = 1 INFO: sorting. INFO: (128 128 60), nframes = 35, ismosaic=0 AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; This looks like an MGH DTI volume MGH DTI SeqPack Info 0 ep_b0#0 0.000000 0 1 ep_b0#1 0.000000 1 2 ep_b0#2 0.000000 2 3 ep_b0#3 0.000000 3 [snip] #@#------------------------------- Eddy/Motion Correct Do Okt 11 18:15:26 CEST 2007 cd /mrt-daten/dt_recon/0001_DTI_RLS2/maps/ectmp eddy_correct /mrt-daten/dt_recon/0001_DTI_RLS2/maps/dwi.nii /mrt-daten/dt_recon/0001_DTI_RLS2/maps/dwi-ec.nii 0 processing vol0000.nii processing vol0001.nii processing vol0002.nii processing vol0003.nii processing vol0004.nii processing vol0005.nii processing vol0006.nii processing vol0007.nii processing vol0008.nii processing vol0009.nii processing vol0010.nii processing vol0011.nii processing vol0012.nii processing vol0013.nii processing vol0014.nii processing vol0015.nii processing vol0016.nii processing vol0017.nii processing vol0018.nii processing vol0019.nii processing vol0020.nii processing vol0021.nii processing vol0022.nii processing vol0023.nii processing vol0024.nii processing vol0025.nii processing vol0026.nii processing vol0027.nii processing vol0028.nii processing vol0029.nii processing vol0030.nii processing vol0031.nii processing vol0032.nii processing vol0033.nii processing vol0034.nii #@#------------------------------- Fitting Tensors Do Okt 11 18:57:54 CEST 2007 cd /mrt-daten/dt_recon/0001_DTI_RLS2 mri_glmfit --y /mrt-daten/dt_recon/0001_DTI_RLS2/maps/dwi-ec.nii --glmdir /mrt-daten/dt_recon/0001_DTI_RLS2/maps --dti /mrt-daten/dt_recon/0001_DTI_RLS2/maps/dwi-infodump.dat $Id: mri_glmfit.c,v 1.138.2.1 2007/09/12 15:38:19 nicks Exp $ cwd /mrt-daten/dt_recon/0001_DTI_RLS2 cmdline mri_glmfit --y /mrt-daten/dt_recon/0001_DTI_RLS2/maps/dwi-ec.nii --glmdir /mrt-daten/dt_recon/0001_DTI_RLS2/maps --dti /mrt-daten/dt_recon/0001_DTI_RLS2/maps/dwi-infodump.dat sysname Linux hostname ixneurol247.med.uni-marburg.de machine i686 user surfer FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /mrt-daten/dt_recon/0001_DTI_RLS2/maps/dwi-ec.nii logyflag 1 X /mrt-daten/dt_recon/0001_DTI_RLS2/maps/dwi-infodump.dat usedti 1 glmdir /mrt-daten/dt_recon/0001_DTI_RLS2/maps DoFFx 0 Creating output directory /mrt-daten/dt_recon/0001_DTI_RLS2/maps Loading y from /mrt-daten/dt_recon/0001_DTI_RLS2/maps/dwi-ec.nii Using DTI bValue = 1000 nB0 = 5 nDir = 30 GradFile /usr/local/freesurfer/diffusion/mgh-dti-seqpack/gradient_mgh_dti30.gdt Matrix condition is 27.8204 Pruning voxels by frame. Found 972044 voxels in mask Saving mask to /mrt-daten/dt_recon/0001_DTI_RLS2/maps/mask.nii search space = 9.33162e+06 Computing natural log of input DOF = 28 Starting fit and test 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Fit completed in 1.75672 minutes Writing results Saving DTI Analysis Computing fa Computing ra Computing vr Computing adc Computing ivc Computing dwisynth Computing dwires Computing dwi rvar mri_glmfit done #@#------------------------------- Registration Do Okt 11 19:02:55 CEST 2007 setenv SUBJECTS_DIR /mrt-daten/dt_recon/0001_DTI_RLS2 cd /mrt-daten/dt_recon/0001_DTI_RLS2 fslregister --s . --mov /mrt-daten/dt_recon/0001_DTI_RLS2/maps/lowb.nii --reg /mrt-daten/dt_recon/0001_DTI_RLS2/maps/register.dat Log file is /mrt-daten/dt_recon/0001_DTI_RLS2/maps/register.dat.fslregister.log Do Okt 11 19:02:55 CEST 2007 --s . --mov /mrt-daten/dt_recon/0001_DTI_RLS2/maps/lowb.nii --reg /mrt-daten/dt_recon/0001_DTI_RLS2/maps/register.dat $Id: fslregister,v 1.16 2007/07/26 16:52:54 greve Exp $ ixneurol247.med.uni-marburg.de Linux ixneurol247.med.uni-marburg.de 2.6.17-1.2142_FC4smp #1 SMP Tue Jul 11 22:57:02 EDT 2006 i686 i686 i386 GNU/Linux ERROR: /mrt-daten/dt_recon/0001_DTI_RLS2/./mri/brainmask not found

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New UserContributions page on the wiki
by Kevin Teich 11 Oct '07

11 Oct '07

Noticing that many FreeSurfer users have developed their own scripts for automating various tasks, somebody had the idea of adding a user contributions section to our documentation. I've added this page to the Wiki: http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions Please use it to add your scripts and check out what other people are doing. If you have anything else you'd like to add, such as tips or techniques, that might be useful to others, please feel free to do so. To edit a Wiki page, you'll need to create an account; instructions on how to do this can be found on the front page, or here: http://surfer.nmr.mgh.harvard.edu/fswiki/GettingAccess -- Kevin Teich

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midline parcellation bug fix
by Michael Harms 11 Oct '07

11 Oct '07

Hello, The Release Notes of v4.0.0 indicate that one of the bug fixes was "Corrected midline parcellation". Is this a fix that affects the volume segmentation (aseg) or the surface parcellation (aparc)? Is that the fix for what was described in the "Known Issues" of v3.0.5 as "During cortical parcellation, areas of the anterior cingulate cortex (rostral anterior cingulate in the parcellation atlas), are mislabelled as corpus callosum or "unlabelled subcortical". A fix for this is in the works, possibly for the next release." 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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func2roi, roisummary, and different paradigm files
by Cameron Ellis 10 Oct '07

10 Oct '07

Hi all, I am running in stable3 trying to finish up an old analysis. I think the problem I am running into arises because I have 2 separate analyses that are identical except for the paradigm files used but I am looking for verification. One analysis uses paradigm files that define only 3 conditions and the other defines 5 conditions (the original 3 plus 2 more). When I run func2roi-sess on each analysis, and compare the results I obtain using roisummary-sess for the 3 conditions that overlap between the 2 analyses they are very different. I guess the root of my question is: how are the condition values calculated? Are they calculated as offsets from averages of everything that isn't defined as a condition? Would this be why the condition values are different for 2 analyses using different paradigm files with overlapping conditions? I attached two roi summaries for comparison. Thanks in advance! Cameron

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installed fsl with fs 4.0.1 package, but can not run it.
by Zhen Zonglei 10 Oct '07

10 Oct '07

Hi all: I have installed fsl with freesurfer 4.0.1, but some errors were reported when I run fsl: > source new_fs.csh Setting up Enviroment for NewFreeSurfer && new_subjects -------- freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.1 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /nfs/h1/r1/new_soft_test/freesurfer FSFAST_HOME /nfs/h1/r1/new_soft_test/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /nfs/h1/r1/new_soft_test/freesurfer/subjects MNI_DIR /nfs/h1/r1/new_soft_test/freesurfer/mni FSL_DIR /nfs/h1/r1/new_soft_test/freesurfer/fsl >fsl /nfs/h1/r1//new_soft_test/freesurfer/fsl/bin/fslwish: line 17: /nfs/h1/r1/new_soft_test/freesurfer/fsl/extras/bin/fslwish8.4: No such file or directory /nfs/h1/r1/new_soft_test/freesurfer/fsl/bin/fslwish: line 17: exec: /nfs/h1/r1/new_soft_test/freesurfer/fsl/extras/bin/fslwish8.4: cannot execute: No such file or directory Can someone give some cues how to slove this problem? Thanks Zonglei Zhen

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mkanalysis-sess -gui error, help!
by Zhen Zonglei 10 Oct '07

10 Oct '07

Hi, all: When I run mkanalysis-sess -gui, Matlab reported the following error, can someone help me solve the problem ? Thanks very much. Zonglei Zhen >mkanalysis-sess -gui Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] < M A T L A B > Copyright 1984-2002 The MathWorks, Inc. Version 6.5.0.180913a Release 13 Jun 18 2002 Using Toolbox Path Cache. Type "help toolbox_path_cache" for more info. To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> ??? Error using ==> load Unable to read MAT file /nfs/h1/r1/jliu/new_soft_test/freesurfer/fsfast/toolbox/mkanalysis_gui.fig See FILEFORMATS for a list of known file types and the functions used to read them. Error in ==> /nfs/h1/app/matlab/toolbox/matlab/iofun/hgload.m On line 45 ==> fileVars = load(filename,'-mat'); Error in ==> /nfs/h1/app/matlab/toolbox/matlab/graphics/openfig.m On line 89 ==> [figs, oldvis] = hgload(filename, struct('Visible','off')); Error in ==> /nfs/h1/app/matlab/toolbox/matlab/uitools/gui_mainfcn.m (local_openfig) On line 184 ==> gui_hFigure = openfig(name, singleton, 'auto'); Error in ==> /nfs/h1/app/matlab/toolbox/matlab/uitools/gui_mainfcn.m

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Freesurfer October 2007