Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Hi Ubuntu- error on generate stats
by rajeev krishnadas 15 Aug '11

15 Aug '11

Hi all, I am new to Freesurfer (and to linux) and appreciate if you could please help. Just managed to install FS onto Ubuntu 10.10 64 bit. I am going through buckner - tutorial for the group analysis with Qdec. I am at the step where I have to import the aseg and aparc data. I clicked on the "generate stats data tables" button - unfortunately an error showed up. --------------------------------------------------------------------------------------------------------------------------------------------- mkdir -p /usr/local/freesurfer/subjects/qdec/stats_tables/ mkdir: cannot create directory `/usr/local/freesurfer/subjects/qdec': Permission denied ERROR: In /usr/pubsw/packages/KWWidgets/CVS-vtk520/src/vtkKWTkUtilities.cxx, line 230 vtkKWQdecApp (0x36dd3d0): Script: vtkTemp3 GenerateStatsDataTables Returned Error on line 1: Uncaught exception: command failed: mkdir -p /usr/local/freesurfer/subjects/qdec/stats_tables/ Stack trace: Uncaught exception: command failed: mkdir -p /usr/local/freesurfer/subjects/qdec/stats_tables/ while executing "vtkTemp3 GenerateStatsDataTables" ------------------------------------------------------------------------------------------------------------------------------------------------ I was wondering if you could please guide me about what could be the problem and how to overcome it! I went through the archives and saw a similar message before, but I did not understand how the person overcame this problem. Thanks in advance. Rajeev -- Dr Rajeev Krishnadas MBBS, MD, DipNB, MRCPsych|Clinical Lecturer in Psychological Medicine|Sackler Institute of Psychobiological Research|Southern General Hospital|Glasgow|G51 4TF|T: +44(0)141 232 7699|F: +44(0)141 232 7697|M: +44(0)7525343479 http://etanerceptforpsoriasis.moonfruit.com/#/home/4545962633

2 1

recon-all error with nu_correct
by Ahmed, F, Me <fahmed＠sun.ac.za> 15 Aug '11

15 Aug '11

Hello Freesurfer experts, I am having great difficulty in trying to run the recon-all process on some scans of mine. I have tried running it a number of times, to no avail and the error I have gotten most recently is the nu_correct error. I have attached the log for this recon-all and hope someone may be able to help. Also, I was told that there is a way one can upload a particular scan via FTP, is this correct and if so, how does one go about doing this? Thank you! Fatima

4 5

Re: [Freesurfer] Freesurfer Digest, Vol 90, Issue 54
by carolina.mr 15 Aug '11

15 Aug '11

1 0

Contrast vector for gender difference and cortical/age regresion
by Knut J Bjuland 15 Aug '11

15 Aug '11

Hi I wish to produce a contrast vector for two conditions in the tutorials. I wish to make a hypothesis for age verse cortical thickness and gender verse cortical thickness. The contrast vector for age verse cortical thickness is [1 0] where age is the first x and cortical thickness is y. The situation is less clear for the group difference, but I think the contrast vector is [1 0] as the gender is two categories. I think this seems a bit strange and is different than the contrast produce by qdec which is [1 1]. What is the right contrast vector for group difference and regression between cortical thickness and aging? Can Freesurfer produce contrast vector in any package beside Qdec? Knut J

1 0

global mean thickness
by Allison R. Kaup 14 Aug '11

14 Aug '11

Hi all, Please pardon the novice question... but what is the best way to get global mean cortical thickness (i.e. combined across hemispheres)? I have used mris_anatomical_stats to get mean thickness separately for each hemisphere. To get a global mean thickness, would I just take a simple average (RH mean thickness + LH mean thickness)/2? Or, do I need some sort of weighted average to account for hemispheric size diffferences? If so, what would I use as the weight? Thanks! Allison -- Allison R. Kaup, M.S. Psychology Intern, UCSD Medical Center Neuropsychological Assessment / Senior Behavioral Health

2 1

Re: [Freesurfer] Label2label on fsaverage
by Rouhollah Abdollahi 14 Aug '11

14 Aug '11

Dear Bruce If I want to rotate sucli pattern too if it is the same? On Fri, Aug 12, 2011 at 1:10 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > I guess you could rotate the surfaces, save them, then resample the labels > so that they get the new surface coords and sample them into the volume, > then onto the newly created surfaces. Not sure, we haven't ever had to do > anything like this. > > > On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: > > Dear Bruce >> I think the easiest way is to create all surfaces again but with corrected >> and well aligned brain. The next step for me to create new labels from old >> labels based on white surface (90 degree rotated) to new white surface. >> But >> how? Is there any way to do that? I mean like label2label or surf2surf if >> two surfaces are the same but one of them only rotated?! >> >> Bests >> Rouhi >> >> On Fri, Aug 12, 2011 at 12:00 PM, Bruce Fischl < >> fischl(a)nmr.mgh.harvard.edu> >> wrote: >> I don't see how anything would work if it was off by 90deg, but >> I guess you should try it >> >> >> >> On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: >> >> Because I am using a result from a very old experiment >> that done on wrong direction and the orig.mgz s are not >> oriented according to >> freesurfer template. I cannot creat white because all >> results that I have (label files) are on white surface. >> The only way that I think I need to >> realign all surfaces and volume and apply that rotation on >> my label files. >> >> >> On Fri, Aug 12, 2011 at 11:42 AM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> wrote: >> not easily. Why would you need to do such a thing? >> >> >> On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: >> >> Dear Bruce >> >> I have a data set which I can not create the white >> surfaces because all of my results are according to white >> surface. I would >> like to know is >> there any way to rotate all surfaces and volumes and >> labels ... (everything) after finishing recon-all process. >> like 90 degree >> around X axis? >> and apply this rotation to all data set? >> >> Best >> Rouhi >> >> >> On Fri, Aug 12, 2011 at 9:17 AM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> wrote: >> Hi Rouhi >> >> I don't really understand. Are you saying you >> transformed the initial image before giving it to >> recon-all? There is a >> switch to >> mris_register to initialize with the tal xform, >> but we never use it as in pretty extensive tests it didn't >> seem to help. >> mris_register has a very large initial capture >> range due to it's global search, so I would be surprised >> if the initial >> orientation >> was the problem. >> >> cheers >> Bruce >> >> >> On Thu, 11 Aug 2011, Rouhollah Abdollahi wrote: >> >> Dear Bruce >> I think I found the problem. The problem came >> from the original oriantation of T1 image and I think >> mris_register could >> not >> find it itself during >> the recon-all. I added to have initial alignment >> to inflated and the problem solved.( mris_register -curve >> -inflated >> ?h.sphere <template >> target> ?h.sphere.reg ) I think it is very >> important to add it to recon-all because if the user >> doesn't know the real >> oriantation it might make >> such a problem. >> >> Thanks for your quick response. >> >> On Thu, Aug 11, 2011 at 10:45 AM, Rouhollah >> Abdollahi <roohy466(a)gmail.com> wrote: >> Dear Bruce >> >> I am working on Freesurfer 2 caret meshes. >> I am using **FreeSurfer2CaretConvertAndRegi**sterClean.sh >> from Van Essen lab >> to >> create caret >> surfaces. when I look at my subjects' >> surfaces I can see in flat map in caret some of subjects >> sulci patterns are >> really >> distorted >> and I think it is related to >> sphere registration to fsaverage sphere. Beacsue the code >> is using sphere.reg to create >> all >> surfaces. >> for the subjects which I have less >> distortion on sulci pattern I have good data (3 subjects) >> but for the (9 >> subjects) >> rest it seems >> they have problem to register to fsaverage. >> Is there any way that I can be sure that >> sphere.reg properly created? >> >> Thank you very much >> >> Rouhi >> >> >> >> On Thu, Aug 11, 2011 at 4:37 AM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> wrote: >> Try using fsaverage as the trgsubject >> Cheers >> Bruce >> >> >> >> On Aug 10, 2011, at 8:35 PM, Rouhollah >> Abdollahi <roohy466(a)gmail.com> wrote: >> >> > .V1_reg.label --regmethod surface >> --srcsurfreg sphere --trgsurfreg sphere.reg --hemi rh and >> when I tried to load >> the >> output >> label file on fsaverage surface like >> inflated one it shows a lot of point looks like it is not >> deformed properly. Is >> it >> related >> to registration to fsaverage or something >> esle? The question is how I can register the subjects >> surfaces to fsaverage >> surfaces? >> -- With Best Regards Rouhi >> --0015175120c69a3c6804aa2ffb81 Content-Type: text/html; >> charset=ISO-8859-1 >> Content-Transfer-Encoding: quoted-printable >> Dear freesurfer experts >> > >> > I've tried to export my label file from >> individual space to fsaverage space by using this command: >> > >> > mri_label2label --srclabel rh.V1.label >> --srcsubject SUB1 --trgsubject SUB1 --trglabel rh.V1_reg. >> > like it is not deformed properly. >> > Is it related to registration to fsaverage or >> something esle? >> > The question is how I can register the >> subjects surfaces to fsaverage >> >> >> The information in this e-mail is intended only >> for the person to whom it is >> addressed. If you believe this e-mail was sent >> to you in error and the e-mail >> contains patient information, please contact the >> Partners Compliance HelpLine at >> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. If the >> e-mail was sent to you in error >> but does not contain patient information, please >> contact the sender and properly >> dispose of the e-mail. >> >> >> >> >> -- >> With Best Regards >> Rouhollah Abdollahi >> >> >> >> >> >> >> -- >> With Best Regards >> Rouhollah Abdollahi >> >> >> >> >> >> >> >> -- >> With Best Regards >> Rouhollah Abdollahi >> >> >> >> >> >> >> >> -- >> With Best Regards >> Rouhollah Abdollahi >> >> >> >> >> >> >> >> -- >> With Best Regards >> Rouhollah Abdollahi >> >> >> >> >> -- With Best Regards Rouhollah Abdollahi

3 11

configure:34016: error: FATAL: libtix not found. Check config.log. Set LDFLAGS or --with-tcl-dir.
by David Baldo 12 Aug '11

12 Aug '11

configure:34016: error: FATAL: libtix not found. Check config.log. 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-I/usr/pubsw/packages/itk/current/include/InsightToolkit/IO -I/usr/pubsw/packages/itk/current/include/InsightToolkit/Numerics -I/usr/pubsw/packages/itk/current/include/InsightToolkit/Numerics/Statistics -I/usr/pubsw/packages/itk/current/include/InsightToolkit/Review -I/usr/pubsw/packages/itk/current/include/InsightToolkit/SpatialObject -I/usr/pubsw/packages/itk/current/include/InsightToolkit/Utilities -I/usr/pubsw/packages/mni/current/include -I/usr/pubsw/packages/tcltktixblt/current/include -I/usr/pubsw/packages/cppunit/current/include -I/usr/pubsw/packages/vxl/current/include/vxl/core -I/usr/pubsw/packages/vxl/current/include/vxl/vcl -I/usr/pubsw/packages/vxl/current/include/vxl/v3p/netlib -I/usr/pubsw/packages/vxl/current/include/vxl/v3p/netlib/opt -I/usr/X11/include -I/usr/X11R6/include -I/usr/X11/include -I/usr/X11R6/include -I/usr/pubsw/packages/vtk/current/include/vtk-5.1 -I/usr/pubsw/packages/KWWidgets/current/include/KWWidgets' 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FLTK_LIB='' FLTK_LIBS='' GLU_CFLAGS='-I/usr/X11/include -I/usr/X11R6/include' GLU_LIBS='-lGLU -lGL -L/usr/X11/lib -lX11 -lm' GL_CFLAGS='-I/usr/X11/include -I/usr/X11R6/include' GL_LIBS='-lGL -L/usr/X11/lib -lX11 -lm' GREP='/usr/bin/grep' GTS_CFLAGS='' GTS_DIR='' GTS_LIBS='' HAS_GZIP='1' HAS_ZCAT='1' HAVE_ANN_LIBS_FALSE='' HAVE_ANN_LIBS_TRUE='#' HAVE_BOOST_LIBS_FALSE='' HAVE_BOOST_LIBS_TRUE='#' HAVE_COCOA_VTK_LIBS_FALSE='' HAVE_COCOA_VTK_LIBS_TRUE='#' HAVE_CPPUNIT_FALSE='#' HAVE_CPPUNIT_TRUE='' HAVE_FERMI_GPU_FALSE='' HAVE_FERMI_GPU_TRUE='#' HAVE_FLTK_LIBS_FALSE='#' HAVE_FLTK_LIBS_TRUE='' HAVE_GFORTRAN_FALSE='' HAVE_GFORTRAN_TRUE='#' HAVE_GTS_LIBS_FALSE='' HAVE_GTS_LIBS_TRUE='#' HAVE_INTEL_COMPILER_FALSE='' HAVE_INTEL_COMPILER_TRUE='' HAVE_ITK_LIBS_FALSE='#' HAVE_ITK_LIBS_TRUE='' HAVE_LATEX_FALSE='' HAVE_LATEX_TRUE='#' HAVE_MAC_OSX_FALSE='#' HAVE_MAC_OSX_TRUE='' HAVE_MPI_LIBS_FALSE='' HAVE_MPI_LIBS_TRUE='#' HAVE_NIFTI_LIBS_FALSE='' HAVE_NIFTI_LIBS_TRUE='#' HAVE_OPEN64_COMPILER_FALSE='' HAVE_OPEN64_COMPILER_TRUE='#' HAVE_OPENGL='' HAVE_OPENGL_LIBS_FALSE='' HAVE_OPENGL_LIBS_TRUE='' HAVE_OPENMP_FALSE='' HAVE_OPENMP_TRUE='#' HAVE_PETSC_LIBS_FALSE='' HAVE_PETSC_LIBS_TRUE='#' HAVE_VTK_LIBS_FALSE='#' HAVE_VTK_LIBS_TRUE='' HAVE_XMLLINT_FALSE='#' HAVE_XMLLINT_TRUE='' HAVE_XXD_FALSE='#' HAVE_XXD_TRUE='' INSTALL_DATA='${INSTALL} -m 644' INSTALL_PROGRAM='${INSTALL}' INSTALL_SCRIPT='${INSTALL}' INSTALL_STRIP_PROGRAM='$(install_sh) -c -s' ITK_CFLAGS=' -I/usr/pubsw/packages/itk/current/include/InsightToolkit -I/usr/pubsw/packages/itk/current/include/InsightToolkit/Algorithms -I/usr/pubsw/packages/itk/current/include/InsightToolkit/BasicFilters -I/usr/pubsw/packages/itk/current/include/InsightToolkit/Common -I/usr/pubsw/packages/itk/current/include/InsightToolkit/IO -I/usr/pubsw/packages/itk/current/include/InsightToolkit/Numerics -I/usr/pubsw/packages/itk/current/include/InsightToolkit/Numerics/Statistics -I/usr/pubsw/packages/itk/current/include/InsightToolkit/Review -I/usr/pubsw/packages/itk/current/include/InsightToolkit/SpatialObject -I/usr/pubsw/packages/itk/current/include/InsightToolkit/Utilities' ITK_DIR='/usr/pubsw/packages/itk/current' ITK_LIB='/usr/pubsw/packages/itk/current/lib/InsightToolkit' ITK_LIBS='-L/usr/pubsw/packages/itk/current/lib/InsightToolkit' JPEG_CFLAGS='' JPEG_LIBS='' KWWIDGETS_CFLAGS=' -I/usr/pubsw/packages/KWWidgets/current/include/KWWidgets' KWWIDGETS_CXXFLAGS=' -I/usr/pubsw/packages/KWWidgets/current/include/KWWidgets' KWWIDGETS_DIR='/usr/pubsw/packages/KWWidgets/current' KWWIDGETS_LIBS=' -L/usr/pubsw/packages/KWWidgets/current/lib/KWWidgets' LATEX='' LDFLAGS=' -L/usr/X11/lib -lX11 -L/usr/X11/lib -lXmu -dead_strip -L/usr/pubsw/packages/mni/current/lib -L/usr/pubsw/packages/tcltktixblt/current/lib -L/usr/pubsw/packages/vxl/current/lib -L/usr/X11R6/lib -L/usr/X11/lib -lX11 -L/usr/X11/lib -lXmu -Wl,-dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib -lGL -L/usr/X11/lib -lX11 -lm -lGLU -lGL -L/usr/X11/lib -lX11 -lm -L/usr/pubsw/packages/vtk/current/lib -L/usr/pubsw/packages/itk/current/lib/InsightToolkit -L/usr/pubsw/packages/KWWidgets/current/lib/KWWidgets ' LDFLAGS_TCL='' LIBDIRS_MGH='utils rgb unix dicom hipsstubs' LIBOBJS=' error.o lstat.o' LIBS=' -L/usr/X11/lib -lX11 -L/usr/X11/lib -lXmu -ltk -ltcl8.4 -L/usr/X11/lib -lX11 -L/usr/X11/lib -lXmu -lvtkCommon -lstdc++ -lvnl_algo -lvnl -lvolume_io -lminc -lnetcdf -lz -lm ' LIBS_CUDA_MGH='utils/libutils_cuda.a fsgdf/libfsgdf.a rgb/librgb.a unix/libunix.a dicom/libdicom.a hipsstubs/libhipsstubs.a log/liblog.a xml2/libxml2.a jpeg/libjpeg.a tiff/libtiff.a expat/libexpat.a' LIBS_ICC='' LIBS_ITK='/usr/pubsw/packages/itk/current/lib/InsightToolkit/libITKIO.a /usr/pubsw/packages/itk/current/lib/InsightToolkit/libITKAlgorithms.a /usr/pubsw/packages/itk/current/lib/InsightToolkit/libITKCommon.a /usr/pubsw/packages/itk/current/lib/InsightToolkit/libITKNumerics.a /usr/pubsw/packages/itk/current/lib/InsightToolkit/libITKMetaIO.a /usr/pubsw/packages/itk/current/lib/InsightToolkit/libITKniftiio.a /usr/pubsw/packages/itk/current/lib/InsightToolkit/libITKNrrdIO.a /usr/pubsw/packages/itk/current/lib/InsightToolkit/libitkpng.a /usr/pubsw/packages/itk/current/lib/InsightToolkit/libitksys.a /usr/pubsw/packages/itk/current/lib/InsightToolkit/libitktiff.a /usr/pubsw/packages/itk/current/lib/InsightToolkit/libitkv3p_netlib.a /usr/pubsw/packages/itk/current/lib/InsightToolkit/libitkzlib.a /usr/pubsw/packages/itk/current/lib/InsightToolkit/libitkgdcm.a /usr/pubsw/packages/itk/current/lib/InsightToolkit/libitkopenjpeg.a /usr/pubsw/packages/itk/current/lib/InsightToolkit/libitkjpeg8.a /usr/pubsw/packages/itk/current/lib/InsightToolkit/libitkjpeg12.a /usr/pubsw/packages/itk/current/lib/InsightToolkit/libitkjpeg16.a /usr/pubsw/packages/itk/current/lib/InsightToolkit/libITKDICOMParser.a ' LIBS_MGH=' utils/libutils.a fsgdf/libfsgdf.a rgb/librgb.a unix/libunix.a dicom/libdicom.a hipsstubs/libhipsstubs.a log/liblog.a xml2/libxml2.a jpeg/libjpeg.a tiff/libtiff.a expat/libexpat.a' LIBS_MNI='-lnetcdf -lvolume_io -lminc' LIBS_NIFTI='' LIBS_OPEN64='' LIBS_OPENGL='-lGLU -lGL -L/usr/X11/lib -lX11 -lm -L/usr/X11R6/lib -L/usr/X11/lib -lX11 -L/usr/X11/lib -lXmu -Wl,-dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib' LIBS_TCL='' LIBS_TCL_OPENGL='' LIBS_VXL='-lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib' LIBTOOL='$(SHELL) $(top_builddir)/libtool' LIB_BLAS_A='' LIB_BLT='' LIB_BLT_JPEG='-ljpeg' LIB_CRYPT='' LIB_CUDA='' LIB_EXPAT='' LIB_G2C_A='' LIB_GFORTRAN='' LIB_JPEG='' LIB_LAPACK_A='' LIB_TCL='-ltcl8.4' LIB_TIFF='' LIB_TIX='' LIB_TK='-ltk' LIB_UUID_A='' LN_S='ln -s' LTLIBOBJS='' MAKEINFO='${SHELL} /Users/dbrang/stable5/dev/config/missing --run makeinfo' MNI_CFLAGS='-I/usr/pubsw/packages/mni/current/include' MNI_DIR='/usr/pubsw/packages/mni/current' MNI_LIBS='-L/usr/pubsw/packages/mni/current/lib' MOC='' MPI_CFLAGS='' MPI_DIR='' MPI_LIB='' MPI_LIBS='' NIFTI_CFLAGS='' NIFTI_DIR='' NIFTI_LIB='' NIFTI_LIBS='' NMR_INSTALL_FALSE='' NMR_INSTALL_TRUE='#' NVCC='/bin/nvcc' NVCCFLAGS='-arch sm_11 --ptxas-options=-v -g' OBJEXT='o' OPENCL_CFLAGS='-I/System/Library/Frameworks/OpenCL.framework/Headers' OPENCL_LIBS='-framework OpenCL' OS='Darwin' OS_CPPFLAGS='' OS_LDFLAGS='-dead_strip' PACKAGE='freesurfer' PACKAGE_BUGREPORT='freesurfer(a)nmr.mgh.harvard.edu' PACKAGE_NAME='Freesurfer' PACKAGE_STRING='Freesurfer stable5' PACKAGE_TARNAME='freesurfer' PACKAGE_VERSION='stable5' PATH_SEPARATOR=':' PETSC_CFLAGS='' PETSC_DIR='' PETSC_LIB='' PETSC_LIBS='' POW_LIB='' PTHREAD_CC='gcc' PTHREAD_CFLAGS='' PTHREAD_LIBS='' QDEC_BUNDLE_TARGET='qdec_bundle' QMAKE='missing' QT_CFLAGS='' QT_CPPFLAGS='' QT_CXXFLAGS='' QT_DEFINES='' QT_DIR='' QT_INCPATH='' QT_LDFLAGS='' QT_LFLAGS='' QT_LIBS='' QT_PATH='' QT_VERSION_MAJOR='' RANLIB='ranlib' RCC='' SCUBA_BUNDLE_TARGET='scuba_bundle' SET_MAKE='' SHARED_CFLAGS='-fno-common' SHARED_LDFLAGS='-dynamiclib' SHELL='/bin/sh' STRIP='strip' TCL_CFLAGS=' -I/usr/pubsw/packages/tcltktixblt/current/include' TCL_DIR='/usr/pubsw/packages/tcltktixblt/current' TCL_LIB='/usr/pubsw/packages/tcltktixblt/current/lib' TCL_LIBS='-L/usr/pubsw/packages/tcltktixblt/current/lib' TEEM_32BIT='1' TEEM_DIO='0' TEEM_ENDIAN='1234' TEEM_QNANHIBIT='1' TESTS_ENVIRONMENT='' TIFF_CFLAGS='' TIFF_LIBS='' TIXWISH='' UIC='' USE_LOCAL_EXPAT_FALSE='#' USE_LOCAL_EXPAT_TRUE='' USE_LOCAL_JPEG_FALSE='#' USE_LOCAL_JPEG_TRUE='' USE_LOCAL_TIFF_FALSE='#' USE_LOCAL_TIFF_TRUE='' USE_SSE_MATHFUN_FALSE='' USE_SSE_MATHFUN_TRUE='#' VERSION='stable5' VTK_CFLAGS=' -I/usr/pubsw/packages/vtk/current/include/vtk-5.1' VTK_COCOA_CFLAGS='' VTK_COCOA_CXXFLAGS='' VTK_COCOA_DIR='' VTK_COCOA_LIB='NO' VTK_COCOA_LIBS='-LNO' VTK_COCOA_LIB_VTK='' VTK_CXXFLAGS=' -I/usr/pubsw/packages/vtk/current/include/vtk-5.1' VTK_DIR='/usr/pubsw/packages/vtk/current' VTK_EXPAT_LIB='-lexpat' VTK_FREETYPE_LIB='-lfreetype' VTK_JPEG_LIB='-ljpeg' VTK_LIB='/usr/pubsw/packages/vtk/current/lib' VTK_LIBS='-L/usr/pubsw/packages/vtk/current/lib' VTK_LIB_VTK='/usr/pubsw/packages/vtk/current/lib/vtk-5.1' VTK_METAIO_LIB='-lvtkmetaio' VTK_MPEG2ENCODE_LIB='' VTK_PNG_LIB='-lvtkpng' VTK_SQLITE_LIB='' VTK_TIFF_LIB='-ltiff' VTK_VERDICT_LIB='-lverdict' VTK_Z_LIB='-lvtkzlib' VXL_CFLAGS=' -I/usr/pubsw/packages/vxl/current/include/vxl/core -I/usr/pubsw/packages/vxl/current/include/vxl/vcl -I/usr/pubsw/packages/vxl/current/include/vxl/v3p/netlib -I/usr/pubsw/packages/vxl/current/include/vxl/v3p/netlib/opt' VXL_DIR='/usr/pubsw/packages/vxl/current' VXL_LIB='/usr/pubsw/packages/vxl/current/lib' VXL_LIBS='-L/usr/pubsw/packages/vxl/current/lib' WXWIDGETS_CFLAGS='' WXWIDGETS_CXXFLAGS='' WXWIDGETS_DIR='' WXWIDGETS_GL_LIBS='' WXWIDGETS_LIBS='' WXWIDGETS_OPTIONAL_LIBS='' XAWPLUS_CFLAGS='' XAWPLUS_CXXFLAGS='' XAWPLUS_DIR='' XAWPLUS_LIBS='' XMKMF='' XMLLINT='xmllint' XXD='xxd' X_LIBS=' -L/usr/X11/lib -lX11 -L/usr/X11/lib -lXmu' ac_ct_CC='gcc' ac_ct_CXX='g++' ac_ct_F77='gfortran' acx_pthread_config='no' am__fastdepCC_FALSE='#' am__fastdepCC_TRUE='' am__fastdepCXX_FALSE='#' am__fastdepCXX_TRUE='' am__include='include' am__isrc='' am__leading_dot='.' am__quote='' am__tar='tar --format=ustar -chf - "$$tardir"' am__untar='tar -xf -' bindir='${exec_prefix}/bin' build='i386-apple-darwin10.8.0' build_alias='' build_cpu='i386' build_os='darwin10.8.0' build_vendor='apple' datadir='${datarootdir}' datarootdir='${prefix}/share' docdir='${datarootdir}/doc/${PACKAGE_TARNAME}' dvidir='${docdir}' exec_prefix='NONE' gl_cflags='-I/usr/X11R6/include' gl_libs='-L/usr/X11R6/lib -L/usr/X11/lib -lX11 -L/usr/X11/lib -lXmu -Wl,-dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib' host='i386-apple-darwin10.8.0' host_alias='' host_cpu='i386' host_os='darwin10.8.0' host_vendor='apple' htmldir='${docdir}' includedir='${prefix}/include' infodir='${datarootdir}/info' install_sh='$(SHELL) /Users/dbrang/stable5/dev/config/install-sh' libdir='${exec_prefix}/lib' libexecdir='${exec_prefix}/libexec' localedir='${datarootdir}/locale' localstatedir='${prefix}/var' mandir='${datarootdir}/man' mkdir_p='$(top_builddir)/config/install-sh -c -d' oldincludedir='/usr/include' pdfdir='${docdir}' pkgs_includes='' pkgs_libraries='' prefix='NONE' program_transform_name='s,x,x,' psdir='${docdir}' sbindir='${exec_prefix}/sbin' sharedstatedir='${prefix}/com' sysconfdir='${prefix}/etc' target='i386-apple-darwin10.8.0' target_alias='' target_cpu='i386' target_os='darwin10.8.0' target_vendor='apple' ## ----------- ## ## confdefs.h. ## ## ----------- ## #define PACKAGE_NAME "Freesurfer" #define PACKAGE_TARNAME "freesurfer" #define PACKAGE_VERSION "stable5" #define PACKAGE_STRING "Freesurfer stable5" #define PACKAGE_BUGREPORT "freesurfer(a)nmr.mgh.harvard.edu" #define PACKAGE "freesurfer" #define VERSION "stable5" #define STDC_HEADERS 1 #define HAVE_SYS_TYPES_H 1 #define HAVE_SYS_STAT_H 1 #define HAVE_STDLIB_H 1 #define HAVE_STRING_H 1 #define HAVE_MEMORY_H 1 #define HAVE_STRINGS_H 1 #define HAVE_INTTYPES_H 1 #define HAVE_STDINT_H 1 #define HAVE_UNISTD_H 1 #define HAVE_DLFCN_H 1 #define HAVE_DIRENT_H 1 #define STDC_HEADERS 1 #define HAVE_SYS_WAIT_H 1 #define HAVE_ARPA_INET_H 1 #define HAVE_FCNTL_H 1 #define HAVE_FLOAT_H 1 #define HAVE_LIMITS_H 1 #define HAVE_LOCALE_H 1 #define HAVE_MEMORY_H 1 #define HAVE_NETDB_H 1 #define HAVE_NETINET_IN_H 1 #define HAVE_STDDEF_H 1 #define HAVE_STDLIB_H 1 #define HAVE_STRING_H 1 #define HAVE_STRINGS_H 1 #define HAVE_SYS_FILE_H 1 #define HAVE_SYS_IOCTL_H 1 #define HAVE_SYS_PARAM_H 1 #define HAVE_SYS_SOCKET_H 1 #define HAVE_SYS_TIME_H 1 #define HAVE_SYS_TIMEB_H 1 #define HAVE_UNISTD_H 1 #define HAVE_WCTYPE_H 1 #define HAVE_SYS_TYPES_H 1 #define HAVE_STDINT_H 1 #define TIME_WITH_SYS_TIME 1 #define HAVE_PTRDIFF_T 1 #define HAVE_STDLIB_H 1 #define HAVE_UNISTD_H 1 #define HAVE_GETPAGESIZE 1 #define HAVE_MMAP 1 #define HAVE_SYS_SELECT_H 1 #define HAVE_SYS_SOCKET_H 1 #define SELECT_TYPE_ARG1 int #define SELECT_TYPE_ARG234 (fd_set *) #define SELECT_TYPE_ARG5 (struct timeval *) #define RETSIGTYPE void #define HAVE_VPRINTF 1 #define HAVE_FORK 1 #define HAVE_VFORK 1 #define HAVE_WORKING_VFORK 1 #define HAVE_WORKING_FORK 1 #define HAVE__BOOL 1 #define HAVE_STDBOOL_H 1 #define HAVE_BZERO 1 #define HAVE_CALLOC 1 #define HAVE_DUP2 1 #define HAVE_FLOOR 1 #define HAVE_FTIME 1 #define HAVE_GETENV 1 #define HAVE_GETCWD 1 #define HAVE_GETPAGESIZE 1 #define HAVE_GETTIMEOFDAY 1 #define HAVE_ISASCII 1 #define HAVE_MEMMOVE 1 #define HAVE_MEMSET 1 #define HAVE_MKDIR 1 #define HAVE_MUNMAP 1 #define HAVE_POW 1 #define HAVE_PUTENV 1 #define HAVE_RINT 1 #define HAVE_SELECT 1 #define HAVE_SETENV 1 #define HAVE_SQRT 1 #define HAVE_STRCASECMP 1 #define HAVE_STRCHR 1 #define HAVE_STRCSPN 1 #define HAVE_STRDUP 1 #define HAVE_STRERROR 1 #define HAVE_STRNCASECMP 1 #define HAVE_STRRCHR 1 #define HAVE_STRSPN 1 #define HAVE_STRSTR 1 #define HAVE_STRTOL 1 #define HAVE_UNAME 1 #define BYTEORDER 1234 #define FS_OPENCL 1 #define XML_NS 1 #define XML_DTD 1 #define XML_CONTEXT_BYTES 1024 #define HAVE_LIBM 1 #define HAVE_LIBZ 1 #define HAVE_LIBNETCDF 1 #define HAVE_LIBMINC 1 #define HAVE_LIBVOLUME_IO 1 #define HAVE_LIBVNL 1 #define HAVE_LIBVNL_ALGO 1 #define HAVE_LIBVTKCOMMON__LSTDC__ 1 configure: exit 1

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Imaging Genomics Post-Doctoral Fellowship
by Anderson Winkler 12 Aug '11

12 Aug '11

*Imaging Genomics Post-Doctoral Fellowship* ** A postdoctoral fellowship in Imaging Genetics at the Olin Neuropsychiatric Research Center, Institute of Living, and the Department of Psychiatry, Yale University, is currently available. The two-year NIH-funded fellowship, under the direction of Dr. David Glahn, will focus on (1) developing a deeper understanding of the genetic basis of human brain structure and function, (2) performing image analysis on large-scale imaging genomic data sets (>1000) including neuroanatomic, diffusion tensor, and resting state fMRI data, (3) developing novel image analytic approaches for gene discovery, and (4) applying imaging genomic finding and methodologies to the study of neuropsychiatric and addictive disorders. The successful candidate will have a strong methods background in imaging and/or genetics or related fields (neurogenetics, imaging, biomedical engineering, computational neuroscience) coupled with excellent writing skills. Programming experience (e.g. Matlab, shell scripting, C/C++) in Linux/Unix environments is advantageous. MDs, PhDs, or MD/PhDs are all encouraged to apply. The position can begin as early as October 1, 2011. Interested candidates are encouraged to email Dr. David Glahn (david.glahn(a)yale.edu <mailto:david.glahn@yale.edu>), including a cover letter and CV.Three letters of recommendation will be requested from qualified candidates.

1 0

Re: [Freesurfer] Label2label on fsaverage
by Rouhollah Abdollahi 12 Aug '11

12 Aug '11

Dear Bruce I think I found the problem. The problem came from the original oriantation of T1 image and I think mris_register could not find it itself during the recon-all. I added to have initial alignment to inflated and the problem solved.( mris_register -curve -inflated ?h.sphere <template target> ?h.sphere.reg ) I think it is very important to add it to recon-all because if the user doesn't know the real oriantation it might make such a problem. Thanks for your quick response. On Thu, Aug 11, 2011 at 10:45 AM, Rouhollah Abdollahi <roohy466(a)gmail.com>wrote: > Dear Bruce > > I am working on Freesurfer 2 caret meshes. I am using > FreeSurfer2CaretConvertAndRegisterClean.sh from Van Essen lab to create > caret surfaces. when I look at my subjects' surfaces I can see in flat map > in caret some of subjects sulci patterns are really distorted and I think it > is related to sphere registration to fsaverage sphere. > Beacsue the code is using sphere.reg to create all surfaces. for the > subjects which I have less distortion on sulci pattern I have good data (3 > subjects) but for the (9 subjects) rest it seems they have problem to > register to fsaverage. Is there any way that I can be sure that > sphere.reg properly created? > > Thank you very much > > Rouhi > > > > On Thu, Aug 11, 2011 at 4:37 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > >> Try using fsaverage as the trgsubject >> Cheers >> Bruce >> >> >> >> On Aug 10, 2011, at 8:35 PM, Rouhollah Abdollahi <roohy466(a)gmail.com> >> wrote: >> >> > .V1_reg.label --regmethod surface --srcsurfreg sphere --trgsurfreg >> sphere.reg --hemi rh and when I tried to load the output label file on >> fsaverage surface like inflated one it shows a lot of point looks like it is >> not deformed properly. Is it related to registration to fsaverage or >> something esle? The question is how I can register the subjects surfaces to >> fsaverage surfaces? -- With Best Regards Rouhi >> --0015175120c69a3c6804aa2ffb81 Content-Type: text/html; charset=ISO-8859-1 >> Content-Transfer-Encoding: quoted-printable Dear freesurfer experts >> > >> > I've tried to export my label file from individual space to fsaverage >> space by using this command: >> > >> > mri_label2label --srclabel rh.V1.label --srcsubject SUB1 --trgsubject >> SUB1 --trglabel rh.V1_reg. >> > like it is not deformed properly. >> > Is it related to registration to fsaverage or something esle? >> > The question is how I can register the subjects surfaces to fsaverage >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > > > -- > With Best Regards > Rouhollah Abdollahi > > > > -- With Best Regards Rouhollah Abdollahi

2 3

QATools
by Knut J Bjuland 12 Aug '11

12 Aug '11

Hi I have looked at QAtools at https://surfer.nmr.mgh.harvard.edu/fswiki/QATools. But there seem to be some trouble. I have fixed up the wrong file issue but there is problem with my files being in the wrong order. Should I try to reorder the files to reflect the new situation or is there something wrong with my processing of recon-all. Knut J mri/transforms/talairach.xfm mri/rawavg.mgz mri/rawavg.mgz mri/orig.mgz mri/orig.mgz mri/nu.mgz mri/transforms/talairach.auto.xfm mri/transforms/talairach.auto.xfm mri/nu.mgz mri/transforms/talairach.xfm .......... ......... .......... ......... .......... ......... 14 outputfiles_NOTOK

2 1

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