Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30065 discussions

Jin, David S. wants to share the file alreadyexists_recon-all.log with you
by Jin, David S. 07 Mar '18

07 Mar '18

To view alreadyexists_recon-all.log, sign in<https://partnershealthcare-my.sharepoint.com/personal/david_jin_mgh_harvard…> or create an account.

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Collecting 2 T1s Best?
by Alessandra Macbeth 07 Mar '18

07 Mar '18

Hi there, I know in the past, it was recommended to acquire 2 T1 scans so that they could be averaged for better SNR, etc. in order to improve cortical thickness and surface area measurements. Is this still the recommendation? We have a few extra minutes in our scanning protocol and are debating whether to include a 2nd T1. Our parameters are: MPRAGE with .8mm^3 voxel size, slice thickness of .8, FA = 8 degrees, TR = 2400ms, TE = 2.72ms, TI = 1060ms. Best, Alessandra -- Alessandra Macbeth, M.A. Doctoral Candidate - Department of Psychology University of California, Riverside

3 2

lh.BA_exvivo.annot Already Exists Error
by Jin, David S. 07 Mar '18

07 Mar '18

Hi, On our machine, with FS6, when we try to run recon-all, FS throws an error of "lh.BA_exvivo.annot already exists" . However, upon deleting lh.BA_exvivo.annot, it still gives the same error. Has anybody else encountered this? Many thanks, David

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Re: [Freesurfer] FSdev compilation error
by Hoopes, Andrew 07 Mar '18

07 Mar '18

Hi Victor, Can you send over the config.log? Also, it’s probably worth noting that the cuda dev builds are currently failing due to recent mrisurf.c changes (working on fixing this now), so if you’re trying to resolve this as soon as possible, it might make sense to checkout and build an older version. best Andrew On March 7, 2018 at 12:13:12 PM, Victor Hansen (victor.hansen(a)nru.dk<mailto:victor.hansen@nru.dk>) wrote: Hello Bruce I am the one inputting the commands - thanks for your tip about MNI libraries, I managed to point it towards the right location for them. However, the "make" step is now complaining about the PetSC libraries: https://paste.ubuntu.com/p/68G4sBB7DK/ I have tried to point it towards the local libraries with --with-petsc= but then ./configure complains that it can't find them at all. Thank you for your help. -- Best regards Victor Hansen IT support Neurological Research Unit, Rigshospitalet nru.dk On Wed, 2018-03-07 at 10:24 -0500, Bruce Fischl wrote: Hi Mel (and Victor?) the missing functions are all from the MNI lib. Not sure what you are missing. Maybe Andrew (ccd) knows? cheers Bruce On Wed, 7 Mar 2018, Melanie Ganz wrote: Dear list, In order to use a brandnew Nvidia GPU we downloaded FSdev and are trying to compile it locally with a new CUDA version. We get all the way to the configure command described on http://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page which is: ./configure --disable-Werror --with-cuda=/usr/local/cuda-9.1 --with-pkgs-dir=/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages --enable-fermi-gpu --libdir=/usr/lib64 Then there are no errors about any libraries, but instead errors about "undefined reference" in the files utils/mri.c and utils/mriio.c (see error below). I searched in the archives and couldn’t find anything about this. Any ideas? Cheers, Mel make[2]: Entering directory '/indirect/data2/Ganz/FSdev/freesurfer/mri_gdfglm' /bin/sh ../libtool --tag=CC --mode=link g++ -I../include -fdata-sections -ffunction-sections -Wl,--gc-sections -L/indirect/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/qt/current/lib -L/usr/lib64 -L/usr/X11R6/lib64 -fopenmp -fdata-sections -ffunction-sections -Wl,--gc-sections -Wl,-Map,ld_map.txt-Wl,--no-demangle -L/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/vxl/current/lib -L/data2/Ganz/FSdev/freesurfer/ce ntos6-x86_64-packages/itk/current/lib/InsightToolkit -o mri_gdfglm mri_gdfglm.o fsgdf.o ../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 ../minc_1_5_1/libminc_1_5_1.a ../netcdf_3_6_0_p1/libnetcdf_3_6_0_p1.a/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKIO.a /data2/Ganz/FSdev/freesurfer/ centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKAlgorithms.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packa ges/itk/current/lib/InsightToolkit/libITKCommon.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insi ghtToolkit/libITKNumerics.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKMetaI O.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKniftiio.a /data2/Ganz/FSdev /freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKNrrdIO.a /data2/Ganz/FSdev/freesurfer/centos6-x86_ 64-packages/itk/current/lib/InsightToolkit/libitkpng.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib /InsightToolkit/libitksys.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitktiff. a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkv3p_netlib.a /data2/Ganz/FSde v/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkzlib.a /data2/Ganz/FSdev/freesurfer/centos6-x86_6 4-packages/itk/current/lib/InsightToolkit/libitkgdcm.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib /InsightToolkit/libitkopenjpeg.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitk jpeg8.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkjpeg12.a /data2/Ganz/FS dev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkjpeg16.a /data2/Ganz/FSdev/freesurfer/centos6-x 86_64-packages/itk/current/lib/InsightToolkit/libITKDICOMParser.a /usr/lib64/libuuid.so -lrt -lz -lm -lcrypt -ldl -lpthread -lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib libtool: link: g++ -I../include -fdata-sections -ffunction-sections -Wl,--gc-sections -fopenmp -fdata-sections -ffunction-sections -Wl,--gc-sections -Wl,-Map -Wl,ld_map.txt -Wl,--no-demangle -o mri_gdfglm mri_gdfglm.o fsgdf.o /usr/lib64/libuuid.so -L/indirect/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/qt/current/lib -L/usr/lib64 -L/usr/X11R6/lib64 -L/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/vxl/current/lib -L/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit ../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 ../minc_1_5_1/libminc_1_5_1.a ../netcdf_3_6_0_p1/libnetcdf_3_6_0_p1.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKIO.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKAlgorithms.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKCommon.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKNumerics.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKMetaIO.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKniftiio.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKNrrdIO.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkpng.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitksys.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitktiff.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkv3p_netlib.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkzlib.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkgdcm.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkopenjpeg.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkjpeg8.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkjpeg12.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkjpeg16.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKDICOMParser.a -lrt -lz -lm -lcrypt -ldl -lpthread -lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib -fopenmp ../utils/libutils.a(mri.o): In function `MRIfree': /data2/Ganz/FSdev/freesurfer/utils/mri.c:5802: undefined reference to `delete_general_transform' ../utils/libutils.a(mri.o): In function `MRIcopyHeader': /data2/Ganz/FSdev/freesurfer/utils/mri.c:6069: undefined reference to `copy_general_transform' /data2/Ganz/FSdev/freesurfer/utils/mri.c:6072: undefined reference to `get_linear_transform_ptr' /data2/Ganz/FSdev/freesurfer/utils/mri.c:6073: undefined reference to `get_inverse_linear_transform_ptr' /data2/Ganz/FSdev/freesurfer/utils/mri.c:6067: undefined reference to `delete_general_transform' ../utils/libutils.a(mriio.o): In function `corRead': /data2/Ganz/FSdev/freesurfer/utils/mriio.c:1611: undefined reference to `input_transform_file' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:1612: undefined reference to `get_linear_transform_ptr' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:1613: undefined reference to `get_inverse_linear_transform_ptr' ../utils/libutils.a(mriio.o): In function `mincRead': /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2316: undefined reference to `start_volume_input' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2321: undefined reference to `get_volume_n_dimensions' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2335: undefined reference to `get_volume_n_dimensions' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2346: undefined reference to `get_volume_sizes' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2355: undefined reference to `get_volume_nc_data_type' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2386: undefined reference to `get_volume_separations' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2425: undefined reference to `convert_voxel_to_world' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2475: undefined reference to `get_voxel_to_world_transform' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2476: undefined reference to `get_linear_transform_ptr' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2456: undefined reference to `input_more_of_volume' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2463: undefined reference to `get_volume_voxel_value' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2485: undefined reference to `delete_volume_input' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2486: undefined reference to `delete_volume' ../utils/libutils.a(mriio.o): In function `mghRead': /data2/Ganz/FSdev/freesurfer/utils/mriio.c:11472: undefined reference to `input_transform_file' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:11473: undefined reference to `get_linear_transform_ptr' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:11474: undefined reference to `get_inverse_linear_transform_ptr' collect2: error: ld returned 1 exit status Makefile:562: recipe for target 'mri_gdfglm' failed make[2]: *** [mri_gdfglm] Error 1 make[2]: Leaving directory '/indirect/data2/Ganz/FSdev/freesurfer/mri_gdfglm' Makefile:1048: recipe for target 'all-recursive' failed make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory '/indirect/data2/Ganz/FSdev/freesurfer' Makefile:957: recipe for target 'all' failed make: *** [all] Error 2 The information in this e-mail is intended only for the person to whom it is addressed. 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FSdev compilation error
by Melanie Ganz 07 Mar '18

07 Mar '18

Dear list, In order to use a brandnew Nvidia GPU we downloaded FSdev and are trying to compile it locally with a new CUDA version. We get all the way to the configure command described on http://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page which is: ./configure --disable-Werror --with-cuda=/usr/local/cuda-9.1 --with-pkgs-dir=/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages --enable-fermi-gpu --libdir=/usr/lib64 Then there are no errors about any libraries, but instead errors about "undefined reference" in the files utils/mri.c and utils/mriio.c (see error below). I searched in the archives and couldn't find anything about this. Any ideas? Cheers, Mel make[2]: Entering directory '/indirect/data2/Ganz/FSdev/freesurfer/mri_gdfglm' /bin/sh ../libtool --tag=CC --mode=link g++ -I../include -fdata-sections -ffunction-sections -Wl,--gc-sections -L/indirect/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/qt/current/l ib -L/usr/lib64 -L/usr/X11R6/lib64 -fopenmp -fdata-sections -ffunction-sections -Wl,--gc-sections -Wl,-Map,ld_map.txt -Wl,--no-demangle -L/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/vxl/current/lib -L/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insig htToolkit -o mri_gdfglm mri_gdfglm.o fsgdf.o ../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 ../minc_1_5_1/libminc_1_5_1.a ../netcdf_3_6_0_p1/libnetcdf_3_6_0_p1.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libITKIO.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libITKAlgorithms.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libITKCommon.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libITKNumerics.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libITKMetaIO.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libITKniftiio.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libITKNrrdIO.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitkpng.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitksys.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitktiff.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitkv3p_netlib.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitkzlib.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitkgdcm.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitkopenjpeg.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitkjpeg8.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitkjpeg12.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitkjpeg16.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libITKDICOMParser.a /usr/lib64/libuuid.so -lrt -lz -lm -lcrypt -ldl -lpthread -lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib libtool: link: g++ -I../include -fdata-sections -ffunction-sections -Wl,--gc-sections -fopenmp -fdata-sections -ffunction-sections -Wl,--gc-sections -Wl,-Map -Wl,ld_map.txt -Wl,--no-demangle -o mri_gdfglm mri_gdfglm.o fsgdf.o /usr/lib64/libuuid.so -L/indirect/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/qt/current/l ib -L/usr/lib64 -L/usr/X11R6/lib64 -L/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/vxl/current/lib -L/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insig htToolkit ../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 ../minc_1_5_1/libminc_1_5_1.a ../netcdf_3_6_0_p1/libnetcdf_3_6_0_p1.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libITKIO.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libITKAlgorithms.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libITKCommon.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libITKNumerics.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libITKMetaIO.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libITKniftiio.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libITKNrrdIO.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitkpng.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitksys.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitktiff.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitkv3p_netlib.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitkzlib.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitkgdcm.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitkopenjpeg.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitkjpeg8.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitkjpeg12.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitkjpeg16.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libITKDICOMParser.a -lrt -lz -lm -lcrypt -ldl -lpthread -lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib -fopenmp ../utils/libutils.a(mri.o): In function `MRIfree': /data2/Ganz/FSdev/freesurfer/utils/mri.c:5802: undefined reference to `delete_general_transform' ../utils/libutils.a(mri.o): In function `MRIcopyHeader': /data2/Ganz/FSdev/freesurfer/utils/mri.c:6069: undefined reference to `copy_general_transform' /data2/Ganz/FSdev/freesurfer/utils/mri.c:6072: undefined reference to `get_linear_transform_ptr' /data2/Ganz/FSdev/freesurfer/utils/mri.c:6073: undefined reference to `get_inverse_linear_transform_ptr' /data2/Ganz/FSdev/freesurfer/utils/mri.c:6067: undefined reference to `delete_general_transform' ../utils/libutils.a(mriio.o): In function `corRead': /data2/Ganz/FSdev/freesurfer/utils/mriio.c:1611: undefined reference to `input_transform_file' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:1612: undefined reference to `get_linear_transform_ptr' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:1613: undefined reference to `get_inverse_linear_transform_ptr' ../utils/libutils.a(mriio.o): In function `mincRead': /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2316: undefined reference to `start_volume_input' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2321: undefined reference to `get_volume_n_dimensions' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2335: undefined reference to `get_volume_n_dimensions' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2346: undefined reference to `get_volume_sizes' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2355: undefined reference to `get_volume_nc_data_type' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2386: undefined reference to `get_volume_separations' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2425: undefined reference to `convert_voxel_to_world' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2475: undefined reference to `get_voxel_to_world_transform' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2476: undefined reference to `get_linear_transform_ptr' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2456: undefined reference to `input_more_of_volume' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2463: undefined reference to `get_volume_voxel_value' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2485: undefined reference to `delete_volume_input' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:2486: undefined reference to `delete_volume' ../utils/libutils.a(mriio.o): In function `mghRead': /data2/Ganz/FSdev/freesurfer/utils/mriio.c:11472: undefined reference to `input_transform_file' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:11473: undefined reference to `get_linear_transform_ptr' /data2/Ganz/FSdev/freesurfer/utils/mriio.c:11474: undefined reference to `get_inverse_linear_transform_ptr' collect2: error: ld returned 1 exit status Makefile:562: recipe for target 'mri_gdfglm' failed make[2]: *** [mri_gdfglm] Error 1 make[2]: Leaving directory '/indirect/data2/Ganz/FSdev/freesurfer/mri_gdfglm' Makefile:1048: recipe for target 'all-recursive' failed make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory '/indirect/data2/Ganz/FSdev/freesurfer' Makefile:957: recipe for target 'all' failed make: *** [all] Error 2

2 1

trouble shooting: pial surface & wm hypointensities
by Marie Sigmund 07 Mar '18

07 Mar '18

2 2

Compatibility of subcortical and cortical segmentations between Version 5.3 and 6.0
by Nils Opel 07 Mar '18

07 Mar '18

Hi Freesurfer Developers, i am currently collecting structural imaging data from several large cohorts that have been processed using different freesurfer versions (5.3 and 6.0). I would be interested on your experiences regarding compatibility between both versions for subcortical and cortical segmentations. More specifically: would it be appropriate to include subcortical and cortical measures derived from both freesurfer versions (5.3 and 6.0) in the same analysis? Thanks a lot in advance and best regards, Nils

2 1

freeview. crash with undefined symbol: _ZN6QMutex12lockInternalEv when I choose colormap lookup table
by Knut J Bjuland 07 Mar '18

07 Mar '18

Dear Freesurfer export, When I chose colormap to lookup table with bert/mri/aseg.mgz freeview crash with the following message. [New Thread 0x7fffce7f4700 (LWP 78012)] /usr/local/freesurfer60/bin/freeview.bin: symbol lookup error: /usr/local/freesurfer60/bin/freeview.bin: undefined symbol: _ZN6QMutex12lockInternalEv [Thread 0x7fffce7f4700 (LWP 78012) exited] [Thread 0x7fffe219d700 (LWP 77903) exited] [Inferior 1 (process 77899) exited with code 0177] Missing separate debuginfos, use: dnf debuginfo-install libXcursor-1.1.15-1.fc27.x86_64 libcrypt-nss-2.26-26.fc27.x86_64 libgcc-7.3.1-5.fc27.x86_64 libgomp-7.3.1-5.fc27.x86_64 libstdc++-7.3.1-5.fc27.x86_64 pcre-8.41-6.fc27.x86_64 sssd-client-1.16.0-8.fc27.x86_64 Whatcan I do to walkaround this error. I also did ldd /usr/local/freesurfer/bin/freeview.bin ldd /usr/local/freesurfer/bin/freeview.bin linux-vdso.so.1 (0x00007ffe435fe000) libQtScriptTools.so.4 => /usr/local/freesurfer/lib/qt/lib/libQtScriptTools.so.4 (0x00007f5d6dbc9000) libQtScript.so.4 => /usr/local/freesurfer/lib/qt/lib/libQtScript.so.4 (0x00007f5d6d7aa000) libQtOpenGL.so.4 => /usr/local/freesurfer/lib/qt/lib/libQtOpenGL.so.4 (0x00007f5d6d58c000) libQtGui.so.4 => /usr/local/freesurfer/lib/qt/lib/libQtGui.so.4 (0x00007f5d6c7da000) libQtCore.so.4 => /usr/local/freesurfer/lib/qt/lib/libQtCore.so.4 (0x00007f5d6c3d5000) libGL.so.1 => /lib64/libGL.so.1 (0x00007f5d6c149000) libXext.so.6 => /lib64/libXext.so.6 (0x00007f5d6bf37000) libvtkverdict.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6 (0x00007f5d6de8d000) libvtkGraphics.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkGraphics.so.5.6 (0x00007f5d6b6cd000) libfreetype.so.6 => /lib64/libfreetype.so.6 (0x00007f5d6b418000) libvtkmetaio.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkmetaio.so.5.6 (0x00007f5d6b290000) libvtkpng.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkpng.so.5.6 (0x00007f5d6b16c000) libvtkzlib.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkzlib.so.5.6 (0x00007f5d6b058000) libvtksqlite.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtksqlite.so.5.6 (0x00007f5d6aeb3000) libvtkImaging.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkImaging.so.5.6 (0x00007f5d6aa2e000) libvtkFiltering.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkFiltering.so.5.6 (0x00007f5d6a59c000) libvtkCommon.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkCommon.so.5.6 (0x00007f5d6a1a7000) libvtksys.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtksys.so.5.6 (0x00007f5d6a067000) libvtkGenericFiltering.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkGenericFiltering.so.5.6 (0x00007f5d69f2b000) libvtkexoIIc.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkexoIIc.so.5.6 (0x00007f5d69de6000) libvtkNetCDF.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkNetCDF.so.5.6 (0x00007f5d69cac000) libvtkVolumeRendering.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkVolumeRendering.so.5.6 (0x00007f5d695fb000) libvtkRendering.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkRendering.so.5.6 (0x00007f5d68fe8000) libvtkftgl.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkftgl.so.5.6 (0x00007f5d68edd000) libvtkWidgets.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkWidgets.so.5.6 (0x00007f5d68be5000) libvtkHybrid.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkHybrid.so.5.6 (0x00007f5d687fd000) libvtkIO.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkIO.so.5.6 (0x00007f5d681c8000) libvtkDICOMParser.so.5.6 => /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkDICOMParser.so.5.6 (0x00007f5d680ab000) libX11.so.6 => /lib64/libX11.so.6 (0x00007f5d67d6d000) librt.so.1 => /lib64/librt.so.1 (0x00007f5d67b65000) libz.so.1 => /lib64/libz.so.1 (0x00007f5d6794e000) libcrypt.so.1 => /lib64/libcrypt.so.1 (0x00007f5d67718000) libdl.so.2 => /lib64/libdl.so.2 (0x00007f5d67514000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f5d672f5000) libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f5d66f6e000) libm.so.6 => /lib64/libm.so.6 (0x00007f5d66c19000) libgomp.so.1 => /lib64/libgomp.so.1 (0x00007f5d669ea000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f5d667d3000) libc.so.6 => /lib64/libc.so.6 (0x00007f5d663f0000) libXrender.so.1 => /lib64/libXrender.so.1 (0x00007f5d661e6000) libfontconfig.so.1 => /lib64/libfontconfig.so.1 (0x00007f5d65fa1000) libgthread-2.0.so.0 => /lib64/libgthread-2.0.so.0 (0x00007f5d65d9f000) libglib-2.0.so.0 => /lib64/libglib-2.0.so.0 (0x00007f5d65a8b000) libpng12.so.0 => /lib64/libpng12.so.0 (0x00007f5d65865000) libSM.so.6 => /lib64/libSM.so.6 (0x00007f5d6565d000) libICE.so.6 => /lib64/libICE.so.6 (0x00007f5d65441000) libGLX.so.0 => /lib64/libGLX.so.0 (0x00007f5d6520f000) libGLdispatch.so.0 => /lib64/libGLdispatch.so.0 (0x00007f5d64f59000) libbz2.so.1 => /lib64/libbz2.so.1 (0x00007f5d64d48000) libpng16.so.16 => /lib64/libpng16.so.16 (0x00007f5d64b15000) libXt.so.6 => /lib64/libXt.so.6 (0x00007f5d648ad000) libXss.so.1 => /lib64/libXss.so.1 (0x00007f5d646a9000) libXft.so.2 => /lib64/libXft.so.2 (0x00007f5d64492000) libjpeg.so.62 => /lib64/libjpeg.so.62 (0x00007f5d6422a000) libxcb.so.1 => /lib64/libxcb.so.1 (0x00007f5d64002000) libfreebl3.so => /lib64/libfreebl3.so (0x00007f5d63dff000) /lib64/ld-linux-x86-64.so.2 (0x00007f5d6dddc000) libexpat.so.1 => /lib64/libexpat.so.1 (0x00007f5d63bcd000) libpcre.so.1 => /lib64/libpcre.so.1 (0x00007f5d6395a000) libuuid.so.1 => /lib64/libuuid.so.1 (0x00007f5d63755000) libXau.so.6 => /lib64/libXau.so.6 (0x00007f5d63551000) Best regards Knut Jørgen

1 1

Clarification on Interpreting results cont'
by Avideh Gharehgazlou 06 Mar '18

06 Mar '18

Hi, Thank you so much for the clarification, so values listed under “CWP” column in "mc-z.abs.th13.sig.cluster.summary" file are my corrected p-values to be reported? (in this case having run monte carlo for multiple comparison correction) CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. AVIS DE CONFIDENTIALITÉ : Ce message électronique, ainsi que tout fichier qui y est joint, est reserve à l'usage exclusif du destinataire visé et peut contenir des renseignements confidentiels et privilégiés. Toute lecture, utilisation, divulgation ou distribution non autorisée est interdite. Si vous n'êtes pas le destinataire visé, veuillez en aviser l'expéditeur par retour de courriel et détruire toutes les copies du message original.

2 1

Re: [Freesurfer] Clarification on interpreting results
by Douglas N. Greve 06 Mar '18

06 Mar '18

On 03/06/2018 12:03 PM, Douglas N. Greve wrote: > > > On 03/06/2018 10:14 AM, Avideh Gharehgazlou wrote: >> Hi, >> >> I have a 2 questions regarding properly interpreting results from >> QDEC. Will you please clarify the following for me? >> >> 1. What is the difference between stats table generated after >> correcting for multiple comparisons (i.e. monte carlo), vs the stats >> table generated after clicking "find clusters and go to max"? Results >> from which stats table should be reported? After searching on the >> web, I am still unclear about what exactly "find clusters and go to >> max" button does... and whether these are corrected results or not? > That button just finds clusters an will move the cursor to the maximum > value inside the cluster. There is no correction for multiple > comparisons with the "find clusters and go to max" button. >> >> 2. My understanding is that "CWP" column in stats table represents >> p-values of each cluster. However, when I manually convert values in >> the "max" column (which I assume are freesurfer p-values reported in >> -log(10)), I get different p-values than what are listed in "CWP" >> column for each cluster. Again, my question is whether I should >> report "CWP" values as my p-values or convert manually myself and >> report those? > The max is the maximum uncorrected vertex-wise significance in the > cluster and is unrelated to the clusterwise p-value (CWP). >> >> I would really appreciate your help! >> >> Thanks so much, >> >> Avi >> >> >> CONFIDENTIALITY NOTICE: This e-mail message, including any >> attachments, is for the sole use of the intended recipient(s) and may >> contain confidential and privileged information. Any unauthorized >> review, use, disclosure or distribution is prohibited. If you are not >> the intended recipient, please contact the sender by reply e-mail and >> destroy all copies of the original message. >> >> AVIS DE CONFIDENTIALITÉ : Ce message électronique, ainsi que tout >> fichier qui y est joint, est reserve à l'usage exclusif du >> destinataire visé et peut contenir des renseignements confidentiels >> et privilégiés. Toute lecture, utilisation, divulgation ou >> distribution non autorisée est interdite. Si vous n'êtes pas le >> destinataire visé, veuillez en aviser l'expéditeur par retour de >> courriel et détruire toutes les copies du message original. >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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