Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

problem with alignment of labeling files generated from the rh.area file
by Tina Jeon 24 May '13

24 May '13

Hello Freesurfers, I have created labeling files from a subject using the area file (previously named base). The label file corresponds to the freesurfer generated cortical label, ctx-rh-bankssts, which I have attached in this email. The labeling files should be the same, however, there are some discrepancies in the files: 1). There is a slight offset in the vertices. 2). A reduced number of vertices in the .label file created from the area file. 3). The vertex numbers are numbered -1. Our goal is to overlay a custom atlas onto a cortical surface generated from amira in freesurfer. Can you please tell how to transform the labeling files so that I can successfully overlay them? I have attached all three files for you. rh.rh_label_2001.label is the labeling file created from the base file, rh.ctx-rh-bankssts.label is the label from freesurfer and the rh.base file I have sent to Bruce the file is too large. When I overlay the rh.rh_label_2001.label and other labels generated from the base file, only parts of the temporal lobe are overlayed. Thank you in advance, Tina Jeon UT Southwestern Medical Center '14 ________________________________ UT Southwestern Medical Center The future of medicine, today.

3 6

A question of running fsfast in mac
by Yongxia Zhou 24 May '13

24 May '13

Dear Freesurfer experts: hi, I'm one of the attendees of the multi-modality training program. I had tried running fsfast in the mac and got an error message. Below is the detail information. Any of your suggestions is highly appreciated and thank you very much. -Sharon OS: Mac OS X 10.5.6 [YongxiaZhous-MacBook:~/Desktop/DICOM/13051914] Young% pwd /Users/Young/Desktop/DICOM/13051914 [YongxiaZhous-MacBook:~/Desktop/DICOM/13051914] Young% selxavg3-sess -s sess01 -analysis /Users/Young/Desktop/DICOM/13051914/sess01/bold/raw/001/test01.sm05.lh -no-preproc -c music_silence.mat -------------------------------------------------------------- selxavg3-sess logfile is /Users/Young/Desktop/DICOM/13051914/log/selxavg3-sess-bold-test01.sm05.lh-130524090501.log -------------------------------------------------------------- ------------------------------------------- /Users/Young/Desktop/DICOM/13051914/sess01 Fri May 24 09:05:02 EDT 2013 anadir = /Users/Young/Desktop/DICOM/13051914/sess01/bold/test01.sm05.lh DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1 ------------------------------------------ ------- 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. < M A T L A B > Copyright 1984-2007 The MathWorks, Inc. Version 7.4.0.287 (R2007a) January 29, 2007 Warning: Duplicate directory name: /Users/Young/matlab. Warning: Function /Users/Young/Downloads/matlab_bgl/test/assert.m has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. Warning: Function /Users/Young/Downloads/matlab_bgl/test/assert.m has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. > In hgrc at 132 In matlabrc at 105 Warning: Function /Users/Young/Downloads/matlab_bgl/test/assert.m has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. > In path at 110 In startup at 5 In matlabrc at 255 Warning: Function /Users/Young/Downloads/matlab_bgl/test/assert.m has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. > In path at 110 In startup at 14 In matlabrc at 255 >> >> >> >> >> >> >> /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> #@# sess01 ############################### /Users/Young/Desktop/DICOM/13051914/sess01 ------------------------- $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m /Applications/freesurfer/fsfast/toolbox/fast_ldanaflac.m /Applications/freesurfer/matlab/MRIread.m ------------------------- outtop = /Users/Young/Desktop/DICOM/13051914 Extension format = nii.gz 1 music_silence.mat ??? Error using ==> MRIread at 76 ERROR: cannot determine format of /Users/Young/Desktop/DICOM/13051914/sess01/bold/001/fmc.siemens.sm5 (MRIread) Error in ==> flac_customize at 87 mri = MRIread(fstem,1); Error in ==> fast_selxavg3 at 65 flac0 = flac_customize(flac0); >> 2013-05-24 09:05:32.710 MATLAB[65661:60b] Process manager already initialized -- can't fully enable headless mode. ------------------------------------------ ERROR: fast_selxavg3() failed\n

2 1

Re: [Freesurfer] command not found
by Louis Nicholas Vinke 24 May '13

24 May '13

Hi Clelia, What do you run to source FS and do you get any output in your terminal after doing so? What operating system are you running? You might try using c-shell instead of bash. -Louis On Fri, 24 May 2013, clelia pellicano wrote: > Hi Louis, > thank you for your answer. > I sourced freesurfer again, but I still get 'command not found'. > What can I try? > Thank you, > > Clelia > > > On Thu, May 23, 2013 at 7:15 PM, Louis Nicholas Vinke <vinke(a)nmr.mgh.harvard.edu> wrote: > Hi Clelia, > If this is in a new terminal then you'll have to source freesurfer again. See here for details: > https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration > -Louis > > On Wed, 22 May 2013, clelia pellicano wrote: > > Hi, > I have run recon-all -s bert -all to try my installation and it worked. > Now, when I try to use other command (and also again recon-all -s bert -all) I always get this: > > dyn1097-8:subjects cpellica$ tkmedit bert orig.mgz > -bash: tkmedit: command not found > dyn1097-8:subjects cpellica$ tkmedit -s bert orig.mgz > -bash: tkmedit: command not found > dyn1097-8:subjects cpellica$ tksurfer -s bert rh pial > -bash: tksurfer: command not found > dyn1097-8:subjects cpellica$ qdec > -bash: qdec: command not found > dyn1097-8:subjects cpellica$ recon-all help > -bash: recon-all: command not found > dyn1097-8:subjects cpellica$ recon-all -s bert -all > -bash: recon-all: command not found > > > I don't know how to do. Please, could you help me? > > Thanks > > Clelia > > > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > > > >

1 0

Rejoindre mon réseau sur LinkedIn
by Melina Papalampropoulou-Tsiridou 24 May '13

24 May '13

LinkedIn ------------ Melina Papalampropoulou-Tsiridou souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de Melina Papalampropoulou-Tsiridou http://www.linkedin.com/e/-qq80um-hh3d1hd2-1o/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… Voir le profil de Melina Papalampropoulou-Tsiridou http://www.linkedin.com/e/-qq80um-hh3d1hd2-1o/rso/228073899/LikC/name/66471… ------------------------------------------ Vous recevez des invitations par e-mail. Cet e-mail est destiné à Freesurfer List. Découvrez pourquoi nous avons inclus ceci : http://www.linkedin.com/e/-qq80um-hh3d1hd2-1o/plh/http%3A%2F%2Fhelp%2Elinke… (c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA.

1 0

freesurfer 5.2 mac download link
by Jonathan Holt 23 May '13

23 May '13

can't seem to find it, would appreciate a link! jon

2 1

Problem with a subject using recon-all command
by stdp82＠virgilio.it 23 May '13

23 May '13

Hi list, I'm performing recon-all -all -notal-check -i $SUBJECTS_DIR/T1_STRUCT.nii.gz -subject SUBJECTS_DIR -cw256 on a T1 with following info:data_type INT16dim1 280dim2 240dim3 240dim4 1datatype 4pixdim1 0.5999908447pixdim2 1.0416666269pixdim3 1.0416666269pixdim4 0.0000000000cal_max 0.0000cal_min 0.0000file_type NIFTI-1+ and I have this error (2) Problem with the least square interpolation for CSF_MAX GLOBAL CSF_MIN=0, CSF_intensity=6, CSF_MAX=55 , nb = 36036 RIGHT_CER CSF_MIN=0, CSF_intensity=6, CSF_MAX=39 , nb = 3042 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=32 , nb = 3852 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=41, CSF_MAX=179 , nb = 14652 LEFT_BRAIN CSF_MIN=0, CSF_intensity=41, CSF_MAX=99 , nb = 14058 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=12 , nb = 432mri_watershed Error: GLOBAL region of the brain empty !Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 recon-all -s SUBJECTS_DIR exited with ERRORS at Fri May 24 00:04:27 CEST 2013 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Complete .log file is also attached. What's happen? Thanks, Stefano

2 1

ERROR: recon-all -subcortseg
by Akio Yamamoto 23 May '13

23 May '13

Hi Freesurfer experts, After installing v5.3.0 (CentOS 6 64bit), the command "recon-all -s test -i sample-001.mgz -i sample-002.mgz -autorecon1" finished without error. Then, when I ran "recon-all -s test -subcortseg", I got the following error: ========== $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --ctab /usr/local/freesurfer/5.3.0/dist/ASegStatsLUT.txt --subject test sysname Linux hostname dhcp006 machine x86_64 user yamamoto UseRobust 0 atlas_icv (eTIV) = 1629767 mm^3 (det: 1.195328 ) MRISread(/home/yamamoto/freesurfer/5.3.0/dist/subjects/test/surf/lh.white): could not open file ========== I encountered this error in v5.2.0, and am still having the same error in v5.3.0. Is this a known issue? I attached the recon-all.log file. Any help is greatly appreciated. Best, Akio

3 4

recon-all failed with errors
by Cat Chong 23 May '13

23 May '13

Dear Experts, I am able to to initiate recon-all but it fails at various stages during the recon-all process even though I should have plenty memory available to run the process. This is the error message I am getting and below is the log file. I am using the freesurfer-Darwin-lion-stable-pub-v5.3.0 on a Mac OSX Lion 10.7.5 INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu May 23 14:05:55 MST 2013 /home/m117348/Documents/Schwedt_MRI/1004_out/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n Darwin r5007111.mayo.edu 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 recon-all -s 1004_out exited with ERRORS at Thu May 23 14:06:26 MST 2013 ------------------------------------- FREESURFER_HOME /Applications/freesurfer/ Actual FREESURFER_HOME /Applications/freesurfer build-stamp.txt: freesurfer-Darwin-lion-stable-pub-v5.3.0 Darwin r5007111.mayo.edu 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 256 memorylocked unlimited maxproc 709 PhysMem: 1987M wired, 5293M active, 2487M inactive, 9767M used, 22G free. ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks(a)aspasia.local (i686-apple-darwin10.2.0) on 2010-02-26 at 14:19:30 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ####################################### GCADIR /Applications/freesurfer//average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /Applications/freesurfer//average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /home/m117348/Documents/Schwedt_MRI/1004_out \n mri_convert /home/m117348/Documents/Schwedt_MRI/1004.mgz /home/m117348/Documents/Schwedt_MRI/1004_out/mri/orig/001.mgz \n mri_convert /home/m117348/Documents/Schwedt_MRI/1004.mgz /home/m117348/Documents/Schwedt_MRI/1004_out/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/m117348/Documents/Schwedt_MRI/1004.mgz... TR=2400.00, TE=3.16, TI=1000.00, flip angle=8.00 i_ras = (0.0109648, -0.99885, 0.0466696) j_ras = (-0.0118836, -0.0467993, -0.998834) k_ras = (-0.999869, -0.0103974, 0.0123829) writing to /home/m117348/Documents/Schwedt_MRI/1004_out/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Thu May 23 14:05:27 MST 2013 Found 1 runs /home/m117348/Documents/Schwedt_MRI/1004_out/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. \n cp /home/m117348/Documents/Schwedt_MRI/1004_out/mri/orig/001.mgz /home/m117348/Documents/Schwedt_MRI/1004_out/mri/rawavg.mgz \n /home/m117348/Documents/Schwedt_MRI/1004_out \n mri_convert /home/m117348/Documents/Schwedt_MRI/1004_out/mri/rawavg.mgz /home/m117348/Documents/Schwedt_MRI/1004_out/mri/orig.mgz --conform \n mri_convert /home/m117348/Documents/Schwedt_MRI/1004_out/mri/rawavg.mgz /home/m117348/Documents/Schwedt_MRI/1004_out/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/m117348/Documents/Schwedt_MRI/1004_out/mri/rawavg.mgz... TR=2400.00, TE=3.16, TI=1000.00, flip angle=8.00 i_ras = (0.0109648, -0.99885, 0.0466696) j_ras = (-0.0118836, -0.0467993, -0.998834) k_ras = (-0.999869, -0.0103974, 0.0123829) Original Data has (1, 1, 1) mm size and (256, 256, 176) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/m117348/Documents/Schwedt_MRI/1004_out/mri/orig.mgz... \n mri_add_xform_to_header -c /home/m117348/Documents/Schwedt_MRI/1004_out/mri/transforms/talairach.xfm /home/m117348/Documents/Schwedt_MRI/1004_out/mri/orig.mgz /home/m117348/Documents/Schwedt_MRI/1004_out/mri/orig.mgz \n INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu May 23 14:05:55 MST 2013 /home/m117348/Documents/Schwedt_MRI/1004_out/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n Darwin r5007111.mayo.edu 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 recon-all -s 1004_out exited with ERRORS at Thu May 23 14:06:26 MST 2013 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Re: [Freesurfer] Siemens dicom error on mri_convert
by Douglas N Greve 23 May '13

23 May '13

Is it straight off the scanner? It does not have the siemens ascii header which usually means that it has been manipulated in some way. You can try using mri_convert with --it dicom doug On 05/23/2013 12:57 PM, Cat Chong wrote: > no it has not. > > > ------------------------------------------------------------------------ > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *To:* freesurfer(a)nmr.mgh.harvard.edu > *Sent:* Thursday, May 23, 2013 9:43 AM > *Subject:* Re: [Freesurfer] Siemens dicom error on mri_convert > > has this file been anonymized? > On 05/23/2013 12:39 PM, Cat Chong wrote: > > Hello Experts, > > I am trying to run the mri_convert command prior to the recon-all > > command on Siemens T1 dicoms (as suggested in the archives). I am > > using freesurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0, > > Mac OS X Lion 10.7.5 > > I am using the command below: > > mri_convert -it siemens_dicom -ot mgz 1002/IM-0001-0001.dcm 2001.mgz > > Below is the command line error I receive, it is a similar error I > > receive when I try to use the command recon-all on the Siemens dicoms. > > I have used freesurfer before on GE dicoms and never had a problem > > running recon-all. Is this error message particular to the Siemens > > dicoms, and would you be able to tell me how to proceed? > > Thank you very much for you help, > > Cat > > reading from 1002/IM-0001-0001.dcm... > > Getting Series No > > Scanning Directory > > INFO: Found 130 files in 1002 > > INFO: Scanning for Series Number 2 > > INFO: found 128 files in series > > INFO: loading series header info. > > INFO: sorting. > > RunNo = 1 > > WARNING: Run 1 appears to be truncated > > Files Found: 128, Files Expected (lRep+1): 1 > > FileName 1002/IM-0001-0001.dcm > > Identification > > NumarisVer syngo MR D11 > > ScannerModel Skyra > > PatientName RS-FMRI^RS-FMRI > > Date and time > > StudyDate 20130222 > > StudyTime 082109.140000 > > SeriesTime 082812.906000 > > AcqTime 082237.315000 > > Acquisition parameters > > PulseSeq *tfl3d1_16ns > > Protocol SAG MP Rage > > PhEncDir ROW > > EchoNo 1 > > FlipAngle 8 > > EchoTime 3.03 > > InversionTime 1000 > > RepetitionTime 2400 > > PhEncFOV 0 > > ReadoutFOV 0 > > Image information > > RunNo 1 > > SeriesNo 2 > > ImageNo 1 > > NImageRows 256 > > NImageCols 256 > > NFrames 128 > > SliceArraylSize 0 > > IsMosaic 1 > > ImgPos -78.6002 128.0000 93.1332 > > VolRes 1.0000 1.0000 1.2500 > > VolDim 0 0 0 > > Vc -0.0000 -1.0000 0.0000 > > Vr -0.0000 -0.0000 -1.0000 > > Vs 0.0000 0.0000 0.0000 > > VolCenter 0.0000 0.0000 0.0000 > > TransferSyntaxUID 1.2.840.10008.1.2.1 > > WARNING: file 1002/IM-0001-0001.dcm does not contain a Siemens ASCII > > header > > has this file been anonymized? > > ERROR: cannot unpack mosiacs without ASCII header > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom > it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline > <http://www.partners.org/complianceline>. If the e-mail was sent to > you in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

2 1

Contrast vector & link with folder name and QDEC-generated sentence
by Tudor Popescu 23 May '13

23 May '13

Hello, I was wondering whether someone could please explain exactly how values are assigned to each column of the design matrix, when a C.dat contrast vector (e.g. [0, 0, 1, -1]) is created, in the "correlation" as opposed to in the "intercept" types of contrasts ... I am asking this because I have a hard time understanding how does a contrast's automatically-created namesake folder (which includes the keywords 'Avg'/'Diff'/'X' and 'Intercept'/'Cor'), such as "lh-Diff-group1-group2-Cor-thickness-behaviouralMeasure", as well as its phrasing in QDEC ("Does the thickness-age correlation differ between group1 and group2?"), exactly correspond to that C.dat vector. Many thanks! Tudor

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