Freesurfer March 2018

freesurfer@nmr.mgh.harvard.edu

115 participants
161 discussions

Question regarding recon-all
by Levitas, Daniel 08 Mar '18

08 Mar '18

Hello, I am running recon-all for the first time, and I am wondering when it is proper to use the -i option. My current recon-all command includes the -i option: recon-all -i T1.nii.gz -s 1020 -all, where T1.nii.gz is a nifti file of all 160 anatomical dicoms. I've seen some commands like this however: recon-all -s subjid -all?. My question is, is it safer to specify the input, and if I choose not to, do I need to create an mri/orig/001.mgz file from mri_convert? Thank you for the help, Dan

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FreeSurfer Edit Sequence Inquiry
by David S Lee 08 Mar '18

08 Mar '18

Hello FreeSurfer Group, I am writing to inquire about Editing Sequence. The "Troubleshooting your output" page (https://surfer.nmr.mgh. harvard.edu/fswiki/FsTutorial/TroubleshootingData) explains the edits sequence as brain mask --> wm volume --> white surface --> control points. Do you suggest people to absolutely stick to this particular sequence? Thanks for your time, David

2 1

Eliminate variable which is the same for all patients from FreeSurfer's Design Matrix
by k.ohmstedt＠stud.uni-heidelberg.de 08 Mar '18

08 Mar '18

Dear all, I am trying to correlate psychometric measurements and the local Gyrification Index. To do so, I use the FreeSurfer pipeline to calculate the lGI and then PALM, following the advice in this thread (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-March/050703.ht…) All my subjects are part of the same group, so I used a FSGD with the group "main" to create the design matrix and mask for my data that are required by PALM. Having a closer look at the design matrix that was created, I found that there was a variable for the group that was the same for all my patients. As it is the same for all patients, I thought eliminating it would not be a problem. But after re-running PALM without it, there were huge differences in my results and effects were notably larger and more significant. Do any of you have any experience which option is best in this case? Is it a valid choice to eliminate the variable for the group, as it is the same for each patient anyway? Furthermore, would you recommend centering for the design matrix? I found that this can have an impact, but I am lost on in which cases it should be done and in which it shouldn't. Thank you for your help! Best regards Kai Ohmstedt

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[Freesurfer/Freeview cutting]
by Dave Yas 08 Mar '18

08 Mar '18

Hello, Can we cut the surface (for flatting later) in freeview? if yes, how? I cant find a tutorial online for that. tksurfer is not working, it crashes by it self. If i cant use freeview to cut, do you suggest another alternative? thank you

2 1

Brain microstructure MRI postdoc (Italy)
by Jovicich, Jorge 08 Mar '18

08 Mar '18

Hello, We will soon advertise a 2-year postdoctoral fellowship at the MRI Group <http://r.unitn.it/en/cimec/mri> of the Center for Mind/Brain Sciences (CIMeC <http://www.cimec.unitn.it/en>), University of Trento <http://www.unitn.it/en/>, Italy. The focus of this position will involve the development, testing and validation of MRI techniques that allow quantification of tissue microstructure properties. The successful candidate will be part of an international multidisciplinary team developing and applying MRI techniques to study brain structure and function supporting normal higher cognitive function as well as the study of cognitive dysfunction in various neurological and neuropsychiatric conditions (including pre-surgical planning, plasticity in deaf and blind, novel markers sensitive to the progression of neurodegenerative diseases). Facilities: The CIMeC MRI neuroimaging lab will house a Siemens Prisma 3T scanner (tentatively May 2018) designed for research and clinical studies. The position will allow for training opportunities in pulse sequence development, brain anatomy, and translational clinical research. The fellow is expected to be able to work independently as well as part of a multidisciplinary team with supervisory responsibilities of graduate student research. The fellow will support research MRI users, will have opportunities to develop new ideas and advance their own research interests in an international academic environment. Requirements: Minimum qualifications are a doctoral degree in cognitive neurosciences, physics, engineering, computer sciences or related area, strong scientific publication record, and demonstrated expertise in MRI methods development and applications. The ideal candidates should be proficient in programming, such as C++, Matlab. Experience in pulse sequence design, particularly on Siemens platform, and/or image reconstruction will be a plus. Additional requirements include high self-motivation, ability of solving research problems independently, and excellent communication skills. Contact: Interested candidates please contact Jorge Jovicich, Ph.D, MSc., Assistant Professor (jorge.jovicich(a)unitn.it) -- Jorge Jovicich, Ph.D. MR Lab Head Center for Mind/Brain Sciences University of Trento, Via delle Regole, 101 38100 Mattarello (TN) Italy Telephone: +39-0461-28 3064 Fax: +39-0461-28-3066 Email: jorge.jovicich(a)unitn.it MRI Methods Group: http://r.unitn.it/en/cimec/mri CIMEC: http://www.cimec.unitn.it/

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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

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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

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Freesurfer March 2018