Freesurfer November 2007

freesurfer@nmr.mgh.harvard.edu

54 participants
74 discussions

mri_volcluster --ERROR: you must specify a pos or neg sign with --fwhm
by PKUNWAR＠nmr.mgh.harvard.edu 26 Aug '09

26 Aug '09

Hi all, I was going through the FSFAST TUTORIAL from wiki( https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial?action=highlight&v…) I got the follwoing error during mri_volcluster, "NOT Adjusting threshold for 1-tailed test ERROR: you must specify a pos or neg sign with --fwhm" I have fwhm.dat file with 4. something vlaue. Command used, [galen:odd-v-0] (nmr-std-env) mri_volcluster --in tal.rfx.osgm/osgm/sig.nii --thmin 2 --fwhmdat tal.rfx.osgm/fwhm.dat --cwpvalthresh 0.1 --mask tal.rfx.osgm/mask.nii --fsaverage --sum tal.rfx.osgm/osgm/cluster.sum --cwsig tal.rfx.osgm/osgm/cwsig.cluster.nii --out tal.rfx.osgm/osgm/sig.cluster.nii --ocn tal.rfx.osgm/osgm/ocn.cluster.nii without --fwhmdat flag, it gave me another error "ERROR: need csd with --cwsig" will appreciate for help thanks pratap ----------------------------------- FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.0.1-20070927 RedHat release: CentOS release 4.4 (Final) Kernel info: Linux 2.6.9-42.0.3.ELsmp x86_64 NMR Center info (/space/freesurfer exists): machine: galen SUBJECTS_DIR: /autofs/space/galen_003/users/carl/Tutorial/buckner_data/FsFastTutorialData/FSFTUTDIR/subjects PWD: /space/galen/3/users/carl/Tutorial/buckner_data/FsFastTutorialData/FSFTUTDIR/fb1-preproc-study/group-analysis-tut/sm-gamma-fwhm5/odd-v-0

2 1

Checking for spikes
by Brittany Cassidy 06 Aug '08

06 Aug '08

Hello all, I was looking for a general way to check for spiking from Freesurfer or the FSFast stream. Any ideas are appreciated. Thanks! -Brittany

3 3

Matlab and Freesurfer
by Robert Baldwin 09 Mar '08

09 Mar '08

Hello- I am new to Freesurfer and Matlab. I have Matlab 7.4.0 installed on an Intel Mac. I just installed Freesurfer. Now when I start Matlab I get the following warnings: Warning: Name is nonexistent or not a directory: /matlab. In path at 110 In startup at 4 In matlabrc at 255 Warning: Name is non existent or not a directory: /toolbox. In path at 110 In startup at 11 In Matlabrc at 255 I have tried adding the freesurfer folder to these files to the path for matlab, but the error still occurs. Any suggestions on how to get this error to quit? Thanks! -Robert

2 4

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

Surfaces, asegs, aparcs, Subcortical Structures
by James N. Porter 10 Dec '07

10 Dec '07

Hello FreeSurfer Folks- I've seen several threads in the archives discussing the expected inaccuracies in the pial, white, and orig surfaces running through subcortical structures. However, I've been unable to ascertain exactly how much and what kind of inaccuracy is acceptable. It makes sense to me that if the entirety of a structure, say the amygdala, were included or excluded in the pial surface, then it would be easy to adjust later measurements. However, what we see in all of our subjects is a random pattern of half in/half out, with weird shapes, when it comes to the surfaces running in and around subcortical structures. For example, take a look the image at this link. http://www.tc.umn.edu/~norb0062/Amygdala.tiff There you will see the how the hippocampus and amygdala are both half included in the pial surface. Item 1 has a strange guitar-shaped chunk taken out of the amygdala, and item 2 has a triangle and a peanut-shaped area removed. Are these the types of expected and accepted inaccuracies, or is there something afoul here that needs to be corrected? I have one other question regarding the interactions of aseg and surface information. Item 3 in the image points out a section of apparent subdural matter that has been classified as grey matter in the aseg but has been excluded from the pial surface. When the final statistics are spit out of recon-all, is there a section of processing that says something like, "Based on the aseg values my grey matter volume is X, but since Y of that is outside of the pial surface I'll call my total volume X-Y"? Or, is this another item to that requires correction and re-running of recon-all? Many thanks in advance, -- Jim Porter Graduate Student Clinical Science & Psychopathology Research University of Minnesota

4 7

after recon-all.
by Jamie Hanson 30 Nov '07

30 Nov '07

Hey Folks- So I just finished autorecon-all on a few subjects and wanted to do some prelim analyses. On the tutorial pages, there is some talk of using QDEC or FSGD... I couldn't really find a good page contrasting the two... or is there not a difference? Is FSGD just a dated version? And per the tutorial pages, I need to have pre-smoothed fsaverage surfaces using recon-all -s <subjid> -qcache. I keep getting an output of ERROR: cannot find fsaverage in /study/eemri/freesurfer, which is my subject dir. So I switched to doing mris_preproc for each subject. But I keep getting an ERROR: Cannot find fsaverage (output). So what am I doing wrong? Which target should I specify? Best, jamie. -- Jamie L. Hanson Waisman Laboratory for Brain Imaging & Behavior | Child Emotion Research Lab University of Wisconsin - Madison 1500 Highland Avenue Madison, WI 53706 ***Please note my new email: jamielarshanson(a)gmail.com***

2 1

Error message
by Juergen Haenggi 30 Nov '07

30 Nov '07

Dear Freesurfer experts We had a problem with the preprocessing of one subject. The following error occurred: #-------------------------------------------- #@# Intensity Normalization Fri Nov 30 12:41:05 CET 2007 /Applications/freesurfer/subjects/Handball_Vp02/mri \n mri_normalize -g 1 nu.mgz T1.mgz \n using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.225 0.008 -0.123 0.315; 0.032 1.156 0.002 0.516; 0.073 0.044 1.349 -3.397; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 SPLINE_CUBIC_SET - Fatal error! The number of data points N must be at least 2. The input value is 1. Darwin juergen-haenggis-computer.local 8.11.1 Darwin Kernel Version 8.11.1: Wed Oct 10 18:23:28 PDT 2007; root:xnu-792.25.20~1/RELEASE_I386 i386 i386 recon-all exited with ERRORS at Fri Nov 30 12:41:09 CET 2007 What does it mean? How to solve 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) -----------------------------------------------------------

2 1

problem viewing in tksurfer
by Sarah Andersen 29 Nov '07

29 Nov '07

Dear FreeSurfers, I am having a problem viewing in tksurfer: I can only see a sliver of the brain. This sliver will rotate and do everything that tksurfer is supposed to do, but I can't view any more of the brain than a tiny piece of the occipital lobe. I have tried this with several different files, and had the same issue for each of them. Tkmedit, on the other hand, works fine. I am using FreeSurfer stable release v4.0.1 on Windows Vista using a virtual machine. FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4-stable-pub-v4.0.1 RedHat release: CentOS release 5 (Final) Kernel info: Linux 2.6.18-8.1.15.el5 i686 I am working through the on-line tutorial and followed the directions to set my environment to /buckner_data/tutorial_subjs I also set SUBJECTS_DIR to $TUTORIAL_DATA . I am working in $SUBJECTS_DIR. The "which" command gives me /usr/local/freesurfer/bin/tksurfer I ran the command "tksurfer good_output lh inflated". The following is the resulting message. surfer: current subjects dir: /usr/local/freesurfer/subjects/freesurfer_tutorial/buckner_data/tutorial_sub js surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /usr/local/freesurfer/subjects/freesurfer_tutorial/buckner_data/tutorial_sub js surfer: Reading header info from /usr/local/freesurfer/subjects/freesurfer_tutorial/buckner_data/tutorial_sub js/good_output/mri/T1.mgz surfer: vertices=125352, faces=250700 Loading /usr/local/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... In the email archives I have seen a response that mentioned the NVidia graphics card. I checked and my machine does have an NVidia graphics card. Thanks in advance for the help! Sarah Sarah Andersen Research Specialist Dept. of Neurology Dept. of Speech, Language, and Hearing Sciences (520) 621-9878 sander(a)email.arizona.edu

4 6

Another talairach question . . .
by Dan Dillon 29 Nov '07

29 Nov '07

Dear FreeSurfers, In the course of checking my skull-strips I discovered that one of my subjects does not have a T1.mgz because they did not pass the automatic Talairach failure detection. I checked the transformation with tkregister2 and -fstal, and it actually looks quite good; the brain is tilted, but the Talairach brain follows the tilt nicely. Nonetheless, to move things forward I made a few small edits and saved the registration. I then re-ran autorecon1 using the -notalairach option (at the end of the command line) in order to make use of my edits. However, I got the exact same error back-Talairach transformation ***FAILED***--and consequently there's no T1.mgz. I thought that by specifying -notalairach at the end of the command line while running autorecon1, I would be bypassing the Talairach detector and thus would be able to avoid this problem, but I'm obviously wrong. How do I make use of my edited Talairach and get autorecon1 to continue? Thanks in advance, Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: dillon(a)wjh.harvard.edu

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Gradient Non-Linearity Distortion Correction for Allegra 3T
by Sergei Bogdanov 29 Nov '07

29 Nov '07

Dear Freesurfers, I have downloaded grad_unwarp_bash.tar.gz from the NBIRN site and am trying to follow the instructions on http://www.nbirn.net/tools/gradient_non_linearity/index.shtm and https://surfer.nmr.mgh.harvard.edu/fswiki/GradientUnwarping?action=highligh… to create the displacement table for Allegra .. I do have the spherical harmonics expansion file for Allegra .. allegra.coef .. I have done: $ perl gradient_unwarp_converter.pl allegra.coef which created grad_unwarp_tables/allegra.coef Now I am trying to run: $ ./scripts/create_displacement_table siemens allegra and I get: Table names: avanto, sonata, trio, brm, crm If you would like to use a different table name, please contact czanner(at)nmr.mgh.harvard.edu for further information Which table name I should use for Allegra 3T or are there any other options? .. I did contact Silvester but sounds like he's been off the project for a year and might not be able to help ... Thank you, Sergei Bogdanov Research Assistant Lewis Center for Neuroimaging University of Oregon sbogdano(a)uoregon.edu

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Freesurfer November 2007