Freesurfer March 2008

freesurfer@nmr.mgh.harvard.edu

55 participants
81 discussions

analysis of covariance using qdec
by Narly A Golestani 13 Mar '08

13 Mar '08

Dear all, Does qdec allow analyses of covariance, and if so, how? is it possible for example to test the effect of a regressor while controlling for the effect of a particular measure? thanks, best, Narly.

4 4

How to analyze fMRI data with mixed design?
by Zhen Zonglei 13 Mar '08

13 Mar '08

Dear, Dr. Greve: I hope I don't bother you too much. But I'm wondering about how to analyze mixed blocked/event related design with FSFAST. In our experiment, we have two blocked conditions and three event-related conditions in every block. We are not sure how to write the parfiles and construct the model to analyze these data in FSFAST. Please give us some suggestions on this issue. Thanks in advance. Zonglei Zhen

2 3

change brush configuration defaults in tkmedit
by Gonzalo Sanchez Benavides 13 Mar '08

13 Mar '08

Hi all, Is there the possibility to change the default settings in Tools>Configure Brush Info and Tools>Configure Volume Brush in Tkmedit? How can I change it, please? Many thanks in advance Congratulations to developers for this great software. -- Gonzalo Sánchez Benavides

3 4

pre-processing, glmfit, and multiple comparisons
by Nicolas Cherbuin 13 Mar '08

13 Mar '08

Hi, Although the documentation for fs is fantasic there are a few questions I have not been able to answer to my satisfaction. I hope somebody will have some patience left to help me out :-) 1. When using mris_preproc we must provide an fsgd file, it is not clear to me if and how the information in the fsgd file is used in this step. Since this file is required I assume that it is not possible to preprocess the data once with a generic fsgd file and then perform glmfit with different fsgd files but just in case I thought I'd check. 2. Next to the FDR rate in the configuration overlay window there is a "only marked" tick box. How is this meant to be used? 3. I have searched the mailing list and the web but I am still a bit confused about what strategy works best in practice for mutliple comparison correction. My experience so far is that if I use FDR most results disappear.... Thanks Nic

2 1

A problem in analyzing DTI data with dt_recon.
by Zhen Zonglei 13 Mar '08

13 Mar '08

Dear, Dr. Greve: Thanks for your help. Today, when we tried to run the new function of FS in DTI analysis, we got stuck again. The dt_recon command cannot run successfully, and always report us 'MRIresample(): error inverting matrix'. The data is from Siemens Trio 3T system, and has 64 diffusion directions. Before running dt_recon, we have unpacked the DTI dicom data to a specific directory with unpacksdcmdir command. To provide more details, I attach the dt_recon.log file and a DTI image (one direction) to this mail. Please help us again. Thanks again! Zonglei Zhen 2008/3/12, Doug Greve <greve(a)nmr.mgh.harvard.edu>: > > > If you are using the 4-column par file, then just code them as separate, > overlapping events, ie. If condition 1 is the block (lasting 10 sec) and > condition 2 is the event (lasting 2 sec), then > > 0 1 10 1 ---> starts at t=0, lasts 10 sec > 0 2 2 1 ----> starts att=0, lasts 2 sec > 5 2 2 1 ----> starts at t=5, lasts 2 sec > 7 2 2 1 ---> starts at t=7, lasts 2 sec > > The last col of 1s just means that the event weight is one (probably what > you want). > > doug > > > Zhen Zonglei wrote: > > Dear, Dr. Greve: > > I hope I don't bother you too much. But I'm wondering about how to analyze > mixed blocked/event related design with FSFAST. In our experiment, we have > two blocked conditions and three event-related conditions in every block. We > are not sure how to write the parfiles and construct the model to analyze > these data in FSFAST. > > Please give us some suggestions on this issue. > > > > Thanks in advance. > > > > Zonglei Zhen > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Centergreve(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 > >

2 3

measuring insula?
by Bird, Anne 13 Mar '08

13 Mar '08

Hi, My research group is interested in measuring the insula but can't find any direct references to it in the freesurfer wiki. Can one obtain data on the insula using freesurfer? If so, how? Thanks, Anne Anne C. Bird, M.S. Clinical Research Coordinator Memory and Aging Center 350 Parnassus Avenue Suite 706 University of California-San Francisco San Francisco, California 94143 Telephone: 415-476-8592 Email: abird(a)memory.ucsf.edu

2 1

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

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Freesurfer March 2008