Freesurfer August 2011

freesurfer@nmr.mgh.harvard.edu

124 participants
212 discussions

Find point on pial surface closest in 3D space to known Talairach coordinates
by David Painter 16 Aug '11

16 Aug '11

Hi Freesurfers, I'm running a brain stimulation (TMS) study and wish to stimulate points on the pial surface that correspond most closely to known Talairach points (from fMRI studies). I'm wondering the best way to find these points using the beautiful Freesurfer cortical reconstructions. I've extracted pial surfaces for 44 brains using recon-all. I'd like to be able to create a label on the point of the pial surface that corresponds most closely to the Talairach point. I've tried creating a label on the inflated surface and dilating it until it becomes visible on the pial surface. But this method highlights adjacent parts of cortex rather than those closest to the Talairach point. I've also tried importing the pial surface into Matlab using mris_display, increasing the transparency of the pial surface, and superimposing the Talaraich points using a scatterplot... (Incidentally, I've been unable to figure out how to transform from Talaraich space to Freesurfer RAS space. I've tried multiplying TT' x tal, where TT = the Talairach transform matrix from talairach.xfm and tal = the Talairach point. But the points are way off where they should be. What am I doing wrong? In the meantime I've solved this problem by working out the Talairach point within Freesurfer)... Using Matlab to display the pial surface and superimposing the scatterplots is producing the best results so far, but it can be very difficult to recognise different parts on the transparent pial surface and this procedure is far from automated. Any ideas? Thanks so much for your time, David Painter, PhD Queensland Brain Institute University of Queensland Australia

1 0

Dmri_trin error in trac-all
by ana ;osp 15 Aug '11

15 Aug '11

Hello freesurfer users. I'm trying to process a trac-all and it works for a while, but i have always the same error when it going to process the error. this is the end of the message Loading cortex mask from /Applications/freesurfer_v5.1//trctrain/trc032/dlabel/mni/cortex+2mm.nii.gz Processing pathway 1 of 18... Matching streamline ends INFO: Have 4088 non-truncated streamlines (min/mean/max length: 60/99/132) INFO: Center of mass of start points: (97+/-3, 96+/-7, 39+/-13) INFO: Center of mass of midpoints: (111+/-3, 109+/-4, 77+/-7) INFO: Center of mass of end points: (113+/-8, 108+/-9, 140+/-6) INFO: Split streamlines into 26 segments Computing path histograms INFO: Total streamline volume is 38001 voxels Computing prior on underlying anatomy (non-truncated streamlines only) dmri_train(23170) malloc: *** mmap(size=16777216) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Abort Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 I read that is due a problem of snow lepard? and one of the propostision is to fix in the source code? does some can help me? I'm running a macbook pro with snow leopard. 6GB and 2x2.4 quad core intel Thanks for help Ana A. UMASS

2 1

Re: [Freesurfer] [freesurfer] FS5.1 talairach issue
by Myriam Siefert 15 Aug '11

15 Aug '11

Hi Nick, Sorry to bother you but I wondered if you had had the time to take a look at my dataset. Thank you very much, Myriam 2011/8/11 Myriam Siefert <myriamsiefert(a)gmail.com> > Hi Nick, > I just would like to make sure that you had received my data, otherwise I > can send it again possibly by another mean if better. > Thanks a lot for your help > Sincerely, > Myriam > > > 2011/8/10 Myriam Siefert <myriamsiefert(a)gmail.com> > >> Hi Bruce and Nick, >> Thank you so much for taking a look! >> Right now I'm uploading the set on the anonymous ftp server ( >> ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming) : >> talairach_issue.zip. It should appear to you in about 1 hour. >> It contains 2 versions of the same subject, the only difference is that >> OK-J-20bis was run with the -use-mritotal flag. >> Please let me know if there's any problem with the upload or if you need >> anything else. >> Sincerely, >> Myriam >> >> >> >> 2011/8/10 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> >>> >>> Hi Myriam >>> Could you send nick a dataset so he can take a look? >>> Thanks >>> Bruce >>> >>> On Aug 10, 2011, at 10:24 AM, Myriam Siefert <myriamsiefert(a)gmail.com> >>> wrote: >>> >>> >>> Hi freesurfers, >>> >>> I'm currently re-processing with FS5.1 some data that i had already >>> processed with FS5.0 and am experiencing some unexpected issues with the >>> linear talairach transform. >>> >>> - While manually checking with Tkregister, I noticed that some off the >>> subjects had quite unsatisfying transforms , while no talairach failure was >>> detected on the log >>> - The transforms looked ok for those subjects in FS 5.0 >>> - I re-run autorecon1 using the -use-mritotal flag >>> - While still no error in the log file, the transforms usually then look >>> acceptable in Tkregister but completely wrong when talairach.xfm is loaded >>> in tkmedit : transformation in the top or bottom left corners, coronal and >>> transversal views interverted, sagittal views rotated by 90 degrees... >>> This happens for a few (not all) of the subjects that I've re-processed >>> with FS5.1 so far. >>> >>> I'm probably doing something wrong but can't figure out what nor what to >>> do about it. >>> Any advice would be highly appreciated. >>> >>> Thanks in advance >>> >>> Myriam Siefert, MD, MS candidate >>> Visiting scholar in SACNlab Northwestern University >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>> 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. >>> >> >> >

3 5

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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'\''s/^[BCDEGRST] $[^ ]*$ $[^ ]*$$/ {"\2", (lt_ptr) \&\2},/p'\''' lt_cv_sys_global_symbol_to_cdecl='sed -n -e '\''s/^. .* $.*$$/extern int \1;/p'\''' lt_cv_sys_max_cmd_len=65536 lt_lt_cv_prog_compiler_c_o='"yes"' lt_lt_cv_prog_compiler_c_o_CXX='"yes"' lt_lt_cv_prog_compiler_c_o_F77='"yes"' lt_lt_cv_sys_global_symbol_pipe='"sed -n -e '\''s/^.*[ ]\$[BCDEGRST][BCDEGRST]*\$[ ][ ]*\$_\$\$[_A-Za-z][_A-Za-z0-9]*\$\$/\\1 \\2\\3 \\3/p'\''"' lt_lt_cv_sys_global_symbol_to_c_name_address='"sed -n -e '\''s/^: \$[^ ]*\$ \$/ {\\\"\\1\\\", (lt_ptr) 0},/p'\'' -e '\''s/^[BCDEGRST] \$[^ ]*\$ \$[^ ]*\$\$/ {\"\\2\", (lt_ptr) \\&\\2},/p'\''"' lt_lt_cv_sys_global_symbol_to_cdecl='"sed -n -e '\''s/^. .* \$.*\$\$/extern int \\1;/p'\''"' ## ----------------- ## ## Output variables. ## ## ----------------- ## ACLOCAL='${SHELL} /Users/dbrang/stable5/dev/config/missing --run aclocal-1.10' AMDEPBACKSLASH='\' AMDEP_FALSE='#' AMDEP_TRUE='' AMTAR='${SHELL} /Users/dbrang/stable5/dev/config/missing --run tar' ANN_CFLAGS='' ANN_DIR='' ANN_LIB='' ANN_LIBS='' AR='ar' AUTOCONF='${SHELL} /Users/dbrang/stable5/dev/config/missing --run autoconf' AUTOHEADER='${SHELL} /Users/dbrang/stable5/dev/config/missing --run autoheader' AUTOMAKE='${SHELL} /Users/dbrang/stable5/dev/config/missing --run automake-1.10' AWK='awk' BLT_CFLAGS='' BLT_LIBS='' BOOST_CFLAGS='' BOOST_DIR='' BOOST_LIB='' BOOST_LIBS='' BOOST_PO_LIB='' BUILDCUDA_FALSE='' BUILDCUDA_TRUE='#' BUILDOPENCL_FALSE='#' BUILDOPENCL_TRUE='' BYTEORDER='1234' CC='gcc' CCDEPMODE='depmode=gcc3' CCLD='g++' CFLAGS='' CPP='gcc -E' CPPFLAGS='-I/usr/X11/include -I/usr/X11R6/include -gfull -O3 -Wall -Werror -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fast -DDarwin -DANSI -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 -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' CPPUNIT_CFLAGS='-I/usr/pubsw/packages/cppunit/current/include' CPPUNIT_DIR='/usr/pubsw/packages/cppunit/current' CPPUNIT_LIB='/usr/pubsw/packages/cppunit/current/lib' CPPUNIT_LIBS='-L/usr/pubsw/packages/cppunit/current/lib' CPUCAPS='' CPUTYPE='intel-mac' CUDA_CFLAGS='-I/include' CUDA_DIR='' CUDA_LIBS='-L/lib -lcudart' CXX='g++' CXXCPP='g++ -E' CXXDEPMODE='depmode=gcc3' CXXFLAGS='' CYGPATH_W='echo' DEFS='' DEPDIR='.deps' DYNAMIC_LIB_EXT='.dylib' ECHO='/bin/echo' ECHO_C='ECHO_N='' ECHO_T='' EGREP='/usr/bin/grep -E' ENABLE_ITK_APPS_FALSE='#' ENABLE_ITK_APPS_TRUE='' ENABLE_KWWIDGETS_APPS_FALSE='#' ENABLE_KWWIDGETS_APPS_TRUE='' ENABLE_QT_APPS_FALSE='' ENABLE_QT_APPS_TRUE='#' ENABLE_TCLTK_APPS_FALSE='#' ENABLE_TCLTK_APPS_TRUE='' ENABLE_WXWIDGETS_APPS_FALSE='' ENABLE_WXWIDGETS_APPS_TRUE='#' ENABLE_XAWPLUS_APPS_FALSE='' ENABLE_XAWPLUS_APPS_TRUE='#' EXEEXT='' EXPAT_CFLAGS='' EXPAT_LIBS='' F77='gfortran' FCLIBS='-L/usr/lib -lgcc' FFLAGS='-g -O2' FLTK_CXXFLAGS='' FLTK_DIR='' FLTK_LDFLAGS='' 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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Freesurfer August 2011