Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30080 discussions

qdec error (2)
by Gonzalo Sanchez Benavides 13 Mar '08

13 Mar '08

Hi all, I'm trying to run qdec on a SL 4.5: [gonzalo@neuro01 ~]$ uname -a Linux neuro01.pic.es 2.6.9-55.0.12.ELsmp #1 SMP Thu Nov 1 08:41:34 CST 2007 i686 i686 i386 GNU/Linux [gonzalo@neuro01 ~]$ /lib/libc.so.6 GNU C Library stable release version 2.3.4, by Roland McGrath et al. Copyright (C) 2005 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. Compiled by GNU CC version 3.4.5 20051201 (Red Hat 3.4.5-2). Compiled on a Linux 2.4.20 system on 2007-06-05. Available extensions: GNU libio by Per Bothner crypt add-on version 2.1 by Michael Glad and others linuxthreads-0.10 by Xavier Leroy The C stubs add-on version 2.1.2. BIND-8.2.3-T5B NIS(YP)/NIS+ NSS modules 0.19 by Thorsten Kukuk Glibc-2.0 compatibility add-on by Cristian Gafton GNU Libidn by Simon Josefsson libthread_db work sponsored by Alpha Processor Inc Thread-local storage support included. For bug reporting instructions, please see: <http://www.gnu.org/software/libc/bugs.html>. I get these errors after run the design analyze: first: ERROR: In /usr/pubsw/packages/KWWidgets/CVS/src/KWWidgets/vtkKWTkUtilities.cxx, line 221 vtkKWQdecApp (0x8790db8): Script: FsgdfPlot_IsWindowShowing 0 Returned Error on line 1: invalid command name "FsgdfPlot_IsWindowShowing" Stack trace: invalid command name "FsgdfPlot_IsWindowShowing" while executing "FsgdfPlot_IsWindowShowing 0" which I can ignore, and then: ERROR: In /usr/pubsw/packages/KWWidgets/CVS/src/KWWidgets/vtkKWApplication.cxx, line 1182 vtkKWQdecApp (0x87903e0): TclTk error: invalid command name "vtkTemp351" invalid command name "vtkTemp351" while executing "vtkTemp351 FocusInCallback" (command bound to event) ERROR: In /usr/pubsw/packages/KWWidgets/CVS/src/KWWidgets/vtkKWApplication.cxx, line 1182 vtkKWQdecApp (0x87903e0): TclTk error: invalid command name "vtkTemp349" invalid command name "vtkTemp349" while executing "vtkTemp349 FinishEditing" (command bound to event) Looking for the error in archive list, I've seen people experimenting so. Following what you have recommended in http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06821.html, I get a clear ldd: [gonzalo@neuro01 ~]$ tcsh [gonzalo@neuro01 ~]$ source $FREESURFER_HOME/SetUpFreeSurfer.csh [gonzalo@neuro01 ~]$ source /usr/local/freesurfer/SetUpFreeSurfer.csh -------- freesurfer-Linux-rh9-stable-pub-v4.0.2 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni [gonzalo@neuro01 ~]$ source $FREESURFER_HOME/bin/tcl_setup FS_TCL_HOME =/usr/local/freesurfer/lib/tcltktixblt TCLLIBPATH= /usr/local/freesurfer/lib/tcltktixblt/lib [gonzalo@neuro01 ~]$ source $FREESURFER_HOME/bin/vtk_setup [gonzalo@neuro01 ~]$ source $FREESURFER_HOME/bin/kww_setup $ ldd $FREESURFER_HOME/bin/qdec.bin libtix8.1.8.4.so => /usr/local/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.so (0x0053c000) libtk8.4.so => /usr/local/freesurfer/lib/tcltktixblt/lib/libtk8.4.so (0x00aa3000) libtcl8.4.so => /usr/local/freesurfer/lib/tcltktixblt/lib/libtcl8.4.so (0x007c6000) libGLU.so.1 => /usr/X11R6/lib/libGLU.so.1 (0x00173000) libGL.so.1 => /usr/X11R6/lib/libGL.so.1 (0x00d8a000) libX11.so.6 => /usr/X11R6/lib/libX11.so.6 (0x00b8e000) libXmu.so.6 => /usr/X11R6/lib/libXmu.so.6 (0x0063e000) libverdict.so.1.2 => /usr/local/freesurfer/lib/vtk/lib/libverdict.so.1.2 (0x005d8000) libvtkGraphics.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkGraphics.so.5.1 (0x00df8000) libvtkfreetype.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkfreetype.so.5.1 (0x001f1000) libvtkmetaio.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkmetaio.so.5.1 (0x00253000) libvtkpng.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkpng.so.5.1 (0x004c6000) libvtkzlib.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkzlib.so.5.1 (0x00112000) libvtkImaging.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkImaging.so.5.1 (0x06a09000) libvtkFiltering.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkFiltering.so.5.1 (0x05b29000) libvtkCommon.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkCommon.so.5.1 (0x002d9000) libvtksys.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtksys.so.5.1 (0x00123000) libvtkexoIIc.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkexoIIc.so.5.1 (0x004e6000) libvtkNetCDF.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkNetCDF.so.5.1 (0x00d15000) libvtkVolumeRendering.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkVolumeRendering.so.5.1 (0x02dd9000) libvtkRendering.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkRendering.so.5.1 (0x01edd000) libvtkftgl.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkftgl.so.5.1 (0x004a2000) libvtkWidgets.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkWidgets.so.5.1 (0x00653000) libvtkHybrid.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkHybrid.so.5.1 (0x01415000) libvtkIO.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkIO.so.5.1 (0x016bf000) libvtkDICOMParser.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkDICOMParser.so.5.1 (0x008c9000) libvtkVolumeRenderingTCL.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkVolumeRenderingTCL.so.5.1 (0x0057f000) libvtkRenderingTCL.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkRenderingTCL.so.5.1 (0x008e8000) libvtkFilteringTCL.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkFilteringTCL.so.5.1 (0x01b2f000) libvtkWidgetsTCL.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkWidgetsTCL.so.5.1 (0x00c91000) libvtkHybridTCL.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkHybridTCL.so.5.1 (0x0085f000) libvtkGraphicsTCL.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkGraphicsTCL.so.5.1 (0x01c20000) libvtkImagingTCL.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkImagingTCL.so.5.1 (0x009a4000) libvtkIOTCL.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkIOTCL.so.5.1 (0x074fb000) libvtkCommonTCL.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkCommonTCL.so.5.1 (0x075fb000) libKWWidgets.so => /usr/local/freesurfer/lib/KWWidgets/lib/KWWidgets/libKWWidgets.so (0x021be000) libz.so.1 => /usr/lib/libz.so.1 (0x00c7f000) libcrypt.so.1 => /lib/libcrypt.so.1 (0x06365000) libdl.so.2 => /lib/libdl.so.2 (0x00b88000) libpthread.so.0 => /lib/tls/libpthread.so.0 (0x00d76000) libstdc++.so.5 => /usr/lib/libstdc++.so.5 (0x041e2000) libm.so.6 => /lib/tls/libm.so.6 (0x00b63000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x004ad000) libc.so.6 => /lib/tls/libc.so.6 (0x04bf2000) libXext.so.6 => /usr/X11R6/lib/libXext.so.6 (0x00c6f000) libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x0433b000) libXxf86vm.so.1 => /usr/X11R6/lib/libXxf86vm.so.1 (0x001ea000) libXt.so.6 => /usr/X11R6/lib/libXt.so.6 (0x00a33000) libSM.so.6 => /usr/X11R6/lib/libSM.so.6 (0x00d6b000) libICE.so.6 => /usr/X11R6/lib/libICE.so.6 (0x00d51000) libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0x005ae000) libtiff.so.3 => /usr/lib/libtiff.so.3 (0x06480000) libexpat.so.0 => /usr/lib/libexpat.so.0 (0x00607000) /lib/ld-linux.so.2 (0x00a1b000) But I still get the error after running the design analyze. So, could you please recomend us what other posibilities do we have in order to correct the error?¿ TIA, Gonzalo -- Gonzalo Sánchez Benavides

2 2

qdec error in vtkKWApplication.cxx
by Christian Scheel 13 Mar '08

13 Mar '08

Dear FS-Experts, I am trying to run Freesurfer on a Ubuntu 7.10 (Gutsy Gibbon) system and unfortunately I encounter the same problem that Gonzalo Sanchez Benavides and also William McGarry described in earlier emails. Copying the new fsgdfPlot.tcl into the $FREESURFER_HOME/lib/tcl directory stopped the "FsgdfPlot_IsWindowShowing" error but did not save me from getting the other two error messages: /ERROR: In /usr/pubsw/packages/KWWidgets/CVS/src/KWWidgets/vtkKWApplication.cxx, line 1182 vtkKWQdecApp (0x8817de0): TclTk error: invalid command name "vtkTemp349" invalid command name "vtkTemp349" while executing "vtkTemp349 FocusInCallback" (command bound to event) ERROR: In /usr/pubsw/packages/KWWidgets/CVS/src/KWWidgets/vtkKWApplication.cxx, line 1182 vtkKWQdecApp (0x8817de0): TclTk error: invalid command name "vtkTemp347" invalid command name "vtkTemp347" while executing "vtkTemp347 FinishEditing" (command bound to event) / Following the advice given in earlier emails I get: /-------- freesurfer-Linux-rh9-stable-pub-v4.0.2 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /home/christian/Promotion/Tutorial/group_analysis_tutorial MNI_DIR /usr/local/freesurfer/mni christian-laptop:~/Promotion/Tutorial/group_analysis_tutorial> source $FREESURFER_HOME/bin/tcl_setup christian-laptop:~/Promotion/Tutorial/group_analysis_tutorial> source $FREESURFER_HOME/bin/vtk_setup christian-laptop:~/Promotion/Tutorial/group_analysis_tutorial> source $FREESURFER_HOME/bin/kww_setup christian-laptop:~/Promotion/Tutorial/group_analysis_tutorial> ldd $FREESURFER_HOME/bin/qdec.bin linux-gate.so.1 => (0xffffe000) libtix8.1.8.4.so => /usr/local/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.so (0xb7f0a000) libtk8.4.so => /usr/local/freesurfer/lib/tcltktixblt/lib/libtk8.4.so (0xb7e4a000) libtcl8.4.so => /usr/local/freesurfer/lib/tcltktixblt/lib/libtcl8.4.so (0xb7db0000) libGLU.so.1 => /usr/lib/libGLU.so.1 (0xb7d1f000) libGL.so.1 => /usr/lib/libGL.so.1 (0xb7c89000) libX11.so.6 => /usr/lib/libX11.so.6 (0xb7b98000) libXmu.so.6 => /usr/lib/libXmu.so.6 (0xb7b82000) libverdict.so.1.2 => /usr/local/freesurfer/lib/vtk/lib/libverdict.so.1.2 (0xb7b53000) libvtkGraphics.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkGraphics.so.5.1 (0xb7535000) libvtkfreetype.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkfreetype.so.5.1 (0xb74d3000) libvtkmetaio.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkmetaio.so.5.1 (0xb744d000) libvtkpng.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkpng.so.5.1 (0xb742d000) libvtkzlib.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkzlib.so.5.1 (0xb741d000) libvtkImaging.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkImaging.so.5.1 (0xb70ed000) libvtkFiltering.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkFiltering.so.5.1 (0xb6e2e000) libvtkCommon.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkCommon.so.5.1 (0xb6c65000) libvtksys.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtksys.so.5.1 (0xb6c2c000) libvtkexoIIc.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkexoIIc.so.5.1 (0xb6bea000) libvtkNetCDF.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkNetCDF.so.5.1 (0xb6bb6000) libvtkVolumeRendering.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkVolumeRendering.so.5.1 (0xb66b1000) libvtkRendering.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkRendering.so.5.1 (0xb63d0000) libvtkftgl.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkftgl.so.5.1 (0xb63c5000) libvtkWidgets.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkWidgets.so.5.1 (0xb6255000) libvtkHybrid.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkHybrid.so.5.1 (0xb5faa000) libvtkIO.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkIO.so.5.1 (0xb5b3a000) libvtkDICOMParser.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkDICOMParser.so.5.1 (0xb5b1b000) libvtkVolumeRenderingTCL.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkVolumeRenderingTCL.so.5.1 (0xb5aec000) libvtkRenderingTCL.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkRenderingTCL.so.5.1 (0xb5a30000) libvtkFilteringTCL.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkFilteringTCL.so.5.1 (0xb593e000) libvtkWidgetsTCL.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkWidgetsTCL.so.5.1 (0xb58ca000) libvtkHybridTCL.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkHybridTCL.so.5.1 (0xb5869000) libvtkGraphicsTCL.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkGraphicsTCL.so.5.1 (0xb5756000) libvtkImagingTCL.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkImagingTCL.so.5.1 (0xb56e7000) libvtkIOTCL.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkIOTCL.so.5.1 (0xb5661000) libvtkCommonTCL.so.5.1 => /usr/local/freesurfer/lib/vtk/lib/libvtkCommonTCL.so.5.1 (0xb55d4000) libKWWidgets.so => /usr/local/freesurfer/lib/KWWidgets/lib/KWWidgets/libKWWidgets.so (0xb5097000) libz.so.1 => /usr/lib/libz.so.1 (0xb5082000) libcrypt.so.1 => /lib/tls/i686/cmov/libcrypt.so.1 (0xb5054000) libdl.so.2 => /lib/tls/i686/cmov/libdl.so.2 (0xb504f000) libpthread.so.0 => /lib/tls/i686/cmov/libpthread.so.0 (0xb5037000) libstdc++.so.5 => /usr/lib/libstdc++.so.5 (0xb4f7d000) libm.so.6 => /lib/tls/i686/cmov/libm.so.6 (0xb4f58000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0xb4f4d000) libc.so.6 => /lib/tls/i686/cmov/libc.so.6 (0xb4e03000) libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0xb4d0f000) libGLcore.so.1 => /usr/lib/libGLcore.so.1 (0xb4377000) libnvidia-tls.so.1 => /usr/lib/tls/libnvidia-tls.so.1 (0xb4375000) libXext.so.6 => /usr/lib/libXext.so.6 (0xb4367000) libXau.so.6 => /usr/lib/libXau.so.6 (0xb4364000) libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0xb435e000) libXt.so.6 => /usr/lib/libXt.so.6 (0xb430d000) libSM.so.6 => /usr/lib/libSM.so.6 (0xb4305000) libICE.so.6 => /usr/lib/libICE.so.6 (0xb42ed000) libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0xb42cd000) libtiff.so.3 => /usr/lib/libtiff.so.3 (0xb4278000) libexpat.so.0 => /usr/lib/libexpat.so.0 (0xb4258000) /lib/ld-linux.so.2 (0xb7f46000) christian-laptop:~/Promotion/Tutorial/group_analysis_tutorial> /But still the error messages do not want to disappear... Any idea where my mistake might be? I am not sure if this is of any relevance but I have added "setenv XLIB_SKIP_ARGB_VISUALS 1" to my SetUpFreeSurfer.csh as without it I was not able to open Qdec at all. Best wishes and thanks a lot in advance, Christian

3 2

export cortical regions from the annotations and surface files
by Matthew.A.Garlinghouse＠Dartmouth.EDU 12 Mar '08

12 Mar '08

Hi, New to Freesurfer. Is it possible to export specific cortical regions/surfaces from the annotations file in a .nii or analyze image format? Best, Matt

3 2

isxconcat-sess question
by Bill Monaco 12 Mar '08

12 Mar '08

Hi, I wanted to know if it's possible to run isxconcat-sess but have it use a different talairach transform when it calls mri_vol2vol. Currently the default is mri/transforms/talairach.xfm, but I want it to use one I had outputted from a previous processing step - mri/transforms/fsl-ta1.xfm Is there an easy way to do this? Thanks, Bill -- Bill Monaco Research Assistant MGH East - CNY 149 149 13th Street - 2271 Charlestown, MA 02129 617-726-9128

2 2

mri_ca_label segfaults
by Martin Kavec 11 Mar '08

11 Mar '08

Hi, I have an emergency here with recon-all -all on a VIP, which segfaults on mri_ca_label -align -nobigventricles ...I tried to run it from the command line and left out the -nobigventricles argument, since actually the subject has enlarged ventricles, but it didn't help. After running for about 45 minutes the last messages are: 471 hippocampal voxels changed. 1 amygdala voxel changed. pass 1: 96288 changed. image 11: -2.434, PF=1.000 pass 2: 14342 changed. image 11: -2.434, PF=1.000 pass3: 5141 changed. Bus error # The images were acquired with our standard protocol, which yields in 95% successful FS results. I run the analysis (exceptionally) on a MacBook Pro with the latest FS. Thanks a lot in advance, Martin

1 0

mri_glmfit problem
by Nicolas Cherbuin 11 Mar '08

11 Mar '08

Hi, I am analysing structural data with mri_glmfit. After pre-processing I have first used one group variable (gender) with one covariate age. I had no problem processing the data and visualising it in tksurfer. I then tried to add another covariate (measure of immediate recall). So I had in total one group variable and two covariates. I reanalysed the data but got the following error: FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /media/storage2/proc/freesurfer/60_w2/checked/analysis/lh.gender_age_immrec.thickness.10.mgh logyflag 0 usedti 0 FSGD gender_age_immrec_fsgd.txt glmdir lh.gender_age_immrec.glmdir DoFFx 0 Creating output directory lh.gender_age_immrec.glmdir Loading y from /media/storage2/proc/freesurfer/60_w2/checked/analysis/lh.gender_age_immrec.thickness.10.mgh Matrix condition is 12866.7 ERROR: matrix is ill-conditioned or badly scaled, condno = 12866.7 Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. 0.000 1.000 68.000 10.000; 1.000 0.000 65.000 5.000; [trunkated the fsgd file output but it is the same as the one used for the sucessful analysis except for one extra column] After this error I thoroughly checked all my files but could not find anything wrong. So to check I could do an analysis using the extra variable I did another analysis with gender and immrec. This worked without problem. I have attached all my fsgd files and mat files. They all use the same subjects and gender info and only differ by one column. Since permutations worked I cannot fathom why it does not work when all put together. The mri_glmfit syntax used for each analysis was: mri_glmfit --y lh.gender_age_immrec.thickness.10.mgh --fsgd gender_age_immrec_fsgd.txt doss --glmdir lh.gender_age_immrec.glmdir --surf average100 lh --C gender_age_immrec.mat mri_glmfit --y lh.gender_immrec.thickness.10.mgh --fsgd gender_immrec_fsgd.txt doss --glmdir lh.gender_immrec.glmdir --surf average100 lh --C gender_immrec.mat mri_glmfit --y lh.gender_age_immrec.thickness.10.mgh --fsgd gender_age_immrec_fsgd.txt doss --glmdir lh.gender_age_immrec.glmdir --surf average100 lh --C gender_age_immrec.mat I use 4.01 (but also checked with 4.02) under Ubuntu 64 bit on a Xeon machine. Thanks very much for your help Nic

2 3

more de-meaning
by Doug Greve 11 Mar '08

11 Mar '08

Hi Chistophe, I'm not surprised by your results as it is very likely that DIQ and F1 have non-zero means. If you were to demean them, then the no-variable analysis would be the same as the with-variable analysis. I actually just sent an email to the Freesurfer list on this topic of demeaning, and I'm copying the list on this response. The important idea here is the difference between computing/testing the mean response and computing the intercept. The intercept is only meaningful when a continuous variable is present. When you do a statistical test, the results will be different for two possible reasons: 1. The statistical efficiencies are different (due to correlations caused by the non-zero mean of the continuous variable), which will reduce significance. This is always the case. 2. The values being tested (ie, the mean vs the intercept) are possibly different. I say "possibly" here because, scientifically speaking, there may be no effect of your continuous variable, in which case it would not add to the overall mean. In my opinion, the most appropriate way to analyze the data is to leave the means in your continuous variables (ie, do not demean). Here's why. When you believe that a variable is important scientifically, you posit a model with a population effect (parameterized by an intercept) and the continuous variable (parameterized by a slope). BOTH OF THESE PARAMETERS ARE INDEPENDENT OF THE SAMPLE YOU HAVE CHOSEN. Therefore, when you perform statistical tests on these parameters, your results are independent of your sample -- very important when doing science! In contrast, the mean of your sample may be dependent on the sample you have chosen, and so statistical tests may only then apply to your sample. For example, if age adds to the hemodynamic response (HRF), older subjects will have a larger amplitude to their HRF. Let's say you perform an experiment on a group of subjects and find that their mean HRF is significantly different than 0. Someone else tries to replicate your experiment and can't. Upon further examination, your sample was somewhat older than the other which caused your sample to have a higher mean and so achieve significance. When both sets are reanalyzed using age as a nuisance variable, the results are the same. This does not necessarily mean you should not demean your variables, but you just have to be careful what conclusions you draw from it. Note: this applies to variables and regressors -- don't demean your observed raw data (unless you know what you are doing). doug Christophe Destrieux wrote: > Hi Doug > > We are using mri_glmfit to study the influence on 2 factors (DIQ anf > F1) on activations observed within a group of autistic patients. > > We used a fsgdf with only one class (autists), and 2 variables : DIQ > and F1, the matrix was computed using DOSS > > We used the following contrast : > > * "0 1 0", to study the influence of DIQ on activations > * "0 0 1", to study the influence of F1 on activations > > We thought that the contrast 1 0 0 would represent activations of the > whole group independently of F1 or DIQ ; > > For comparison purposes we also computed the same map with one class > but without any variable ; We assumed that the contrast that should > represent activation of the whole group should then be "1" > > We expected the same results in both analysis, but in fac maps are > very different : they look ok with the second analysis (1class, 0 > variable, contrast "1"), but were almost empty with the first one (1 > class, 2 variables, contrast "1 0 0") > > There is probably something wrong but we cant find out where > > thanks > > PS the message is CC to Frederic Andersson who joined the lab a few > weeks ago ; he is engineer and he will probably bug you from time to > time : ) > > cheers > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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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

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cerebellum
by Anthony Dick 07 Mar '08

07 Mar '08

Hello- Are there any plans to implement the cerebellum segmentation of Makris et al. (2005; Neuroimage, 25) as an automated segmentation into part of the freesurfer workflow? Anthony -- Anthony Steven Dick, Ph.D. Post-Doctoral Fellow Human Neuroscience Laboratory Department of Neurology The University of Chicago 5841 S. Maryland Ave. MC-2030 Chicago, IL 60637 Phone: (773)-834-7770 Email: adick(a)uchicago.edu Web: http://home.uchicago.edu/~adick/

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Re: problems with retaining wm edits using -autorecon2-cp flag
by Teddy Youn 06 Mar '08

06 Mar '08

Hi all, another quick question. I don't know if anyone else has encountered this problem, but after making pial, wm and cp edits our group don't seem to retain all our edits. The OtherUsefulFlags wikipage suggests that FS should retain all the edits from a flag that is more upstream in the autorecon2's workflow. We've noticed that a lot of our manual wm edits for some of our brains are lost when we use -autorecon2-cp flag. Has anyone else encountered this problem? Is there a way to prevent this from happening? -Thanks in advance, Teddy Doris Duke Clinical Research Fellow '07-'08 North Texas TBI Research Center UT Southwestern Medical Center at Dallas Warren Alpert School of Medicine at Brown University, MD '09 Teddy.Youn(a)utsouthwestern.edu (401)-714-2847

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