Freesurfer

freesurfer@nmr.mgh.harvard.edu

5 participants
30076 discussions

problems
by 顏鳳賢 14 Dec '07

14 Dec '07

Hi, I had downloaded the freesurfer to my system (Linux Fedora Core 4) and had completed all the installation procedures. Question 1: I would like to convert analyze format to .mgz. What command line do I use? Can I type "mri_convert x249.img 001.mgz "? Question 2: When I type "recon-all -s x249 -nuintensitycor", it doesn't run and has a error" nu_correct." What would I do to resolve the problem? Question 3: It doesn't find talairach.xfm. What would I do to get the file? thanks~~ FreeSurfer problem report --------------------------------------------------------------------- FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4-stable-pub-v4.0.1 RedHat release: Fedora Core release 4 (Stentz) Kernel info: Linux 2.6.11-1.1369_FC4 i686 --------------------------------------------------------------------- 1) subject name x249 2) the entire command-line executed [root@cgu ~]# ksh # tcsh [root@cgu ~]# setenv FREESURFER_HOME /usr/local/freesurfer [root@cgu ~]# source $FREESURFER_HOME/SetUpFreeSurfer.csh [root@cgu ~]# cd $SUBJECTS_DIR [root@cgu subjects]# cd x249/mri/orig [root@cgu orig]# mri_convert x249.img 001.mgz [root@cgu mri]# recon-all -s x249 -nuintensitycor 3) the error message generated ERROR: nu_correct 4) optionally include the subject's /script/recon-all.log Thu Oct 4 13:38:14 CST 2007 /usr/local/freesurfer/subjects/x249 /usr/local/freesurfer/bin/recon-all -s x249 -nuintensitycor subjid x249 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v4.0.1 Linux cgu.edu.tw 2.6.11-1.1369_FC4 #1 Thu Jun 2 22:55:56 EDT 2005 i686 i686 i386 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 32 kbytes maxproc 16383 ######################################## program versions used $Id: recon-all,v 1.133.2.5 2007/09/17 16:38:00 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.7 2007/01/06 00:01:14 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:14-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.4.2 $Id: talairach_avi,v 1.4 2007/05/29 23:24:27 nicks Exp $ mri_convert --version stable4 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:14-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: tkregister2.c,v 1.86.2.1 2007/08/15 15:39:42 nicks Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 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 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_normalize.c,v 1.52 2007/01/02 21:34:40 nicks Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_watershed.cpp,v 1.67 2007/06/29 13:40:47 fischl Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_segment.c,v 1.33 2007/02/14 19:59:27 fischl Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_label2label.c,v 1.33 2007/08/10 18:23:46 greve Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_em_register.c,v 1.57 2006/12/29 02:09:06 nicks Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_ca_normalize.c,v 1.38 2007/01/02 13:37:33 fischl Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_ca_register.c,v 1.63 2007/01/18 22:58:55 nicks Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_ca_label.c,v 1.80 2007/04/13 13:22:32 fischl Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_pretess.c,v 1.16 2007/01/18 20:23:47 nicks Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 unknown option -ALL-INFO ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_fill.c,v 1.111 2007/07/19 20:16:38 fischl Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_tessellate.c,v 1.32 2007/04/26 21:44:21 fischl Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_concatenate_lta.c,v 1.3 2007/05/17 19:56:59 nicks Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_normalize_tp2.c,v 1.6 2007/01/08 18:10:12 nicks Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_smooth.c,v 1.21 2007/01/01 18:16:19 fischl Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_inflate.c,v 1.33.2.2 2007/08/16 01:40:10 nicks Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_curvature.c,v 1.25 2007/07/20 16:42:32 fischl Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_fix_topology.c,v 1.43 2007/01/05 16:57:16 nicks Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_topo_fixer.cpp,v 1.26 2007/02/13 19:30:47 segonne Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_ca_label.c,v 1.23 2007/03/23 20:00:07 fischl Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_euler_number.c,v 1.5 2006/12/29 02:09:10 nicks Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_make_surfaces.c,v 1.99 2007/08/14 01:56:01 fischl Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_register.c,v 1.48 2007/07/19 15:58:50 fischl Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_anatomical_stats.c,v 1.54 2007/08/02 17:37:13 nicks Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mrisp_paint.c,v 1.8 2007/02/13 16:57:23 fischl Exp $ User: root Machine: cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ####################################### GCA RB_all_2007-08-08.gca GCASkull RB_all_withskull_2007-08-08.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs ####################################### #-------------------------------------------- #@# Nu Intensity Correction Thu Oct 4 13:38:15 CST 2007 mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 /usr/local/freesurfer/subjects/x249/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 1.7 2007/01/06 00:01:14 nicks Exp $ Linux cgu.edu.tw 2.6.11-1.1369_FC4 #1 Thu Jun 2 22:55:56 EDT 2005 i686 i686 i386 GNU/Linux Thu Oct 4 13:38:15 CST 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.20457 /usr/local/freesurfer/subjects/x249/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.20457/nu0.mnc mri_convert orig.mgz ./tmp.mri_nu_correct.mni.20457/nu0.mnc Can't find the talairach xform '/usr/local/freesurfer/subjects/x249/mri/transforms/talairach.xfm' Transform is not loaded into mri $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ 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.20457/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Oct 4 13:38:31 CST 2007 nu_correct -clobber ./tmp.mri_nu_correct.mni.20457/nu0.mnc ./tmp.mri_nu_correct.mni.20457/nu1.mnc [root@cgu.edu.tw:/usr/local/freesurfer/subjects/x249/mri/] [2007-10-04 13:38:31] 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_20509/ ./tmp.mri_nu_correct.mni.20457/nu0.mnc ./tmp.mri_nu_correct.mni.20457/nu1.imp /usr/local/freesurfer/mni/bin/volume_stats: error while loading shared libraries: libstdc++.so.5: cannot open shared object file: No such file or directory nu_estimate_np_and_em: crashed while running volume_stats (termination status=32512) nu_correct: crashed while running nu_estimate_np_and_em (termination status=32512) ERROR: nu_correct Linux cgu.edu.tw 2.6.11-1.1369_FC4 #1 Thu Jun 2 22:55:56 EDT 2005 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Thu Oct 4 13:38:32 CST 2007

5 8

using BET prior to recon-all?
by Simon Rushton 14 Dec '07

14 Dec '07

I've been having problems with a few brains (errors during processing). I found advice on the web about running BET (the FSL brain extraction tool) prior to running recon-all http://lcni.uoregon.edu/mediawiki/index.php/SOFT:FSL_FreeSurfer I've tried this and that has helped. (Searching the mail archive I see that at least one other person on this list appears to be doing the same.) My question is, is this a sensible thing to do? I ask because looking at the output I see that at least one of the early processing stages appears to expect a non-stripped brain: mri_watershed -brain_atlas /Applications/freesurfer/average/ RB_all_withskull_2007-08-08.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Does this suggest that I either should not try the BET trick or that if I do that I should make some modifications to the recon-all scripts? simon

4 6

Error message II
by Juergen Haenggi 14 Dec '07

14 Dec '07

Dear FS experts Here I found a warning that seem to be related to the error message I posted before. mri_convert /usr/local/freesurfer/subjects/s237/mri/rawavg.mgz /usr/local/freesurfer/subjects/s237/mri/orig.mgz --conform WARNING ==================++++++++++++++++++++++++================================== ===== The physical sizes are (299.52 mm, 299.52 mm, 176.85 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 300 slices. The freesurfer tools should be able to handle more than 256 slices. If you find problems, please let us know (freesurfer(a)nmr.mgh.harvard.edu) ==================================================++++++++++++++++++++++++== ============= Thanks Regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

2 1

Convert from {png,jpg} --> dicom
by Rudolph Pienaar 14 Dec '07

14 Dec '07

Hi - Does anyone have any advice/experience on converting/creating DICOMS from arbitrary image formats like png or jpg? Basically I have a set of post-processed png images that were derived from a set of DICOMS. I'd like to convert these png images back into DICOM again. Many thanks -=R -- Rudolph Pienaar, M.Eng, D.Eng / email: rudolph(a)nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA

1 0

Error message
by Juergen Haenggi 14 Dec '07

14 Dec '07

Dear FS experts We analysed data with FS 4.0.1. In the past, when analyzed this data with FS 3.0.5 everthing worked fine. Now with FS 4.0.1 an error occurred maybe due to a dimension mismatch. mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 0.971 -0.044 -0.018 10.786; 0.050 1.089 0.053 6.110; 0.023 -0.037 0.908 10.383; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 0.971 -0.044 -0.018 12.779; 0.050 1.089 0.053 1.874; 0.023 -0.037 0.908 12.727; 0.000 0.000 0.000 1.000; reading segmented volume aseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 6094 (min = 350, max = 1400), aspect = 0.84 (min = 0.10, max = 0.75) need search nearby using seed (148, 150, 159), TAL = (-20.0, 31.0, -22.0) talairach voxel to voxel transform 1.028 0.042 0.017 -11.521; -0.046 0.914 -0.055 -4.525; -0.028 0.036 1.099 -11.334; 0.000 0.000 0.000 1.000; segmentation indicates cc at (148, 150, 159) --> (-20.0, 31.0, -22.0) ERROR: mri_fill-MRIcheckVolDims: volume1 height=256 != volume2 height=300. talairach cc position changed to (-20.00, 31.00, -22.00) Erasing brainstem...Linux 130.60.235.1 2.6.9-67.ELsmp #1 SMP Wed Nov 7 13:58:04 EST 2007 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Wed Dec 12 03:34:18 CET 2007 How to fix that problem? Thanks in advance Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

1 0

does one need a separate pediatric atlas for freesurfer?
by Binyam Nardos 13 Dec '07

13 Dec '07

Freesurfers, I had a couple of questions regarding your atlas. I'm working with a children and young adult subject population (ages 7-18). I'm interested in anatomical measures such as cortical thickness, and volumes of different structures. What are your thoughts on what atlas to use for these subjects? Does one need a separate (more representative?) atlas or can one use your default atlas... Also, can Freesurfer accomodate the use of custom-made atlases? appreciate your help, Binyam Binyam Nardos Cognitive Rehabilitation Research Group Washington University School of Medicine Box # 8505 4444 Forest Park Blvd St. Louis, MO 63108 Office: (314) 454-7795 Fax: (314) 286-1601 The contents of this e-mail message and any attachments are intended solely for the addressee(s) named in this message. This communication is intended to be and to remain confidential and may be subject to applicable physician/patient and/or work product privileges. If you are not the intended recipient of this message, or if this message has been addressed to you in error, please immediately alert the sender by reply e-mail and then delete this message and its attachments.

2 1

reading DICOM fields
by Michael Harms 13 Dec '07

13 Dec '07

Hello, Will any of the FS utilities read a Siemens DICOM file and dump the (complete) DICOM header information to the terminal or text file? I've looked at the options for mri_info and unpacksdcmdir, but as far as I can tell neither have this capability. We have a handy Sun executable that can do this, but I've tried without success to locate a Linux executable that could do the same. Does anyone out there know of one? 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 --------------------------------------------------------------------

3 2

General editing questions
by Chris Watson 13 Dec '07

13 Dec '07

Hello, I've been looking through the archives and still have some questions about getting the best data for GM volume, WM volume, and the volumes of each sub-cortical structure. This is lengthy, but I'm trying to save a lot of future man-hours that I wasted on the first dataset I was doing. *1)* I ran recon-all -autorecon-all overnight, not knowing that I could make edits in the middle of the process. Does this mean that, e.g if I need to add control points, I have to do / recon-all -autorecon2-cp -autorecon3, /and then make edits to the new wm.mgz and do /recon-all -autorecon2-wm -autorecon3/, *then* make edits to the pial surface and run everything to the end? Or, if I add control points, then only run recon-all -autorecon2-cp, this will be acceptable? And then edit wm.mgz, and run /recon-all -autorecon2-wm/? And so on? * 2)* This brings me to another head-scratcher for me: wm.mgz. Should all subcortical structures fall within the main surface (including ventral DC)? Sometimes the main surface cuts into the hippocampus/amygdala, so do I have to add/delete voxels so it goes around it? I would think the pial and main surfaces should exclude these two structures. The pial and main surfaces are ~identical around the midline and subcortical structures; is this the desired result? If i want to change the main surface in general, what is the significance of the white voxels vs. grey voxels? I think I understand that the white voxels are there just so the surface will go around it. So, in theory, if I wanted the main surface to include all of the hippocampus, I could fill in white voxels for the hippocampus, and then run recon-all? If I delete grey voxels, will this change the main surface (I suppose this would be like the opposite of control points)? I read in some places that the WM volume produced by mris_anatomical_stats is taken from all the voxels that are "on" in wm.mgz. If this is the case, then the ventricles are included? Some parts of the dura are "on" in wm.mgz (although do not fall within ?h.white); would I have to go slice-by-slice deleting these annoying voxels? * 3)* Is the data from mri_segstats and mri_anatomical_stats reliable? I've seen threads saying mris_wm_volume and mris_volume are better, since the GM and WM data are calculated using the surfaces. I don't have the former (I'm using FS v3.0.4). I noticed the WM volume given by /mris_volume rh.white - /{sum of volumes of subcortical structures} is very close to that given by mri_segstats, which is similar to using mris_wm_volume. Is this correct? So, in the future, when I do recon-all for a subject, is it best to do it step-by-step, and make the edits as I go along? Thanks for the help, Chris

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pial misclassified
by abel cruz vadell 13 Dec '07

13 Dec '07

Hi everyone Checking the automatic pial segmentation of my MRI images in Freesurfer, I found some pixels misclassified as pial surface and I'm afraid of wrong cortical thickness measures in those regions. Is there any automatic tool to correct it? I attached two images with arrows signalizing the problem. Thanks for your help ______________________________________________ ¿Chef por primera vez? Sé un mejor Cocinillas. http://es.answers.yahoo.com/info/welcome

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mris_smooth and 'NoRandomness'
by Michael Harms 12 Dec '07

12 Dec '07

Hello, Is the 'NoRandomness' flag (and -seed flag) no longer relevant for 'mris_smooth'? That is, if I repeat mris_smooth using the same input, I always get the same output smoothed surface, which was not my expectation. Similarly, even if I explicitly chose different -seed values, the output is identical. 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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