Freesurfer May 2019

freesurfer@nmr.mgh.harvard.edu

95 participants
141 discussions

Re: [Freesurfer] problems compiling Freesurfer
by fsbuild 26 May '19

26 May '19

External Email - Use Caution Hello Jorge, You can download a tar archive of the pre-built 3rd party packages with the following command, curl -O http://surfer.nmr.mgh.harvard.edu/pub/data/fspackages/prebuilt/centos7-pack… - and the versions of the contained packages in that archive should work: vtk=5.10.1, petsc=2.3.3; itk=4.13.0; gts=0.7.6; ann=1.1.2 You could set the individual cmake variables for each package, or instead try setting -DFS_PACKAGES_DIR to point to the absolute path of where the ./packages subdir is after expanding the archive; then you should not have to individually set ITK_DIR, VTK_DIR, etc. You could also try downloading “makefile.wiki” from, https://drive.google.com/file/d/1IMEWQty_7zjsglbErQOlu_KpXb8Lmgmv/view to do this and other work for you. Then if you type “make -f makefile.wiki pkg_download” it will try to download that package archive for you, and also add a python3 (needed for freesurfer) from anaconda python under the packages archive.  If it finds everything, it will generate the cmake command for you.  You can see what the command will be with  "make -f makefile.wiki config_print”.  You can also use it to try and run cmake, then do the build and install passes - type “make -f makefile.wiki help” to read more. - R. On May 26, 2019, at 04:25, Jorge Naranjo <jorge.naranjo(a)nyu.edu> wrote:        External Email - Use Caution        Hi All,IM compiling freesurfer, after many bumps reached a point i havent figured out how to proceed.My setup:Centos7 GCC 4.8.5 Freesurfer 6.0.0 Dependencies as in /usr/pubsw/packages/ - KWWWidgets :  CVS-vtk560- petsc : 2.3.3-p13- mni 1.5- tcltktixblt : 8.4.6 - wxWidgets  wxGTK-2.8.9 - xawplus: 3.1.0 Dependencies I built and installed in  /usr/pubsw/packages/- dcmtk: 3.6.4- itk: 4.9.1- vxl: v1.17.0The rest of dependencies installed through RPM packages (yum) system-wise.. including VTK, etc ... then I do:FS_PACKAGES_DIR=/usr/pubsw/packagesVTK_DIR=/usrVTK_LIBRARIES=/usr/lib64PREFIX=/share/apps/NYUAD3/freesurfer/6..0.0CMAKE_BUILD_TYPE=ReleasePETSC_DIR=/usr/pubsw/packages/petsc/currentITK_DIR=/usr/pubsw/packages/itk/4.9.1/lib/cmake/ITK-4.9/OpenGL_GL_PREFERENCE=GLVNDDANN_LIBRARIES=/usr/lib64export CPATH=$CPATH:/usr/pubsw/packages/itk/4.9.1/include/ITK-4.9/ cmake3 ../freesurfer -DFS_PACKAGES_DIR=${FS_PACKAGES_DIR} -DVTK_LIBRARIES=${VTK_LIBRARIES}  -DVTK_DIR=${VTK_DIR} -DCMAKE_INSTALL_PREFIX=${PREFIX} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -DPETSC_DIR=${PETSC_DIR} -DITK_DIR=${ITK_DIR} -DOpenGL_GL_PREFERENCE=${OpenGL_GL_PREFERENCE} -DANN_LIBRARIES=${DANN_LIBRARIES} -DUSE_PYTHON_INCLUDE_DIR=ON -DCMAKE_EXE_LINKER_FLAGS="-L/usr/lib64/ -lglut"makeNOTE: the glut thing is because if I let the system use the libglut inside packages dir in the source code ... compilation  breaks with :/bin/ld: ../packages/glut/libglut.a(glut_win.c.o): undefined reference to symbol 'glXCreateContextWithConfigSGIX'Well, the thing is that will all the above, the compilation breaks with this message:[ 57%] Built target trk_tools[ 57%] Built target streamlineFilter[ 57%] Built target testOrientationPlanesFromParcellation[ 57%] Building CXX object anatomicuts/CMakeFiles/dmri_match.dir/AnatomiCuts_correspondences.cxx.o/scratch/apps/singularity-sandboxes/braimcore-sandbox/SOFTWARE/FREESURFER/freesurfer/anatomicuts/AnatomiCuts_correspondences.cxx: In function ‘int main(int, char**)’:/scratch/apps/singularity-sandboxes/braimcore-sandbox/SOFTWARE/FREESURFER/freesurfer/anatomicuts/AnatomiCuts_correspondences.cxx:648:62: error: expected primary-expression before ‘double’    vcl_vector<unsigned int> assign = vnl_hungarian_algorithm<double>( distances ); //.GetAssignmentVector();                                                              ^make[2]: *** [anatomicuts/CMakeFiles/dmri_match.dir/AnatomiCuts_correspondences.cxx.o] Error 1make[1]: *** [anatomicuts/CMakeFiles/dmri_match.dir/all] Error 2make: *** [all] Error 2Any help !?? will be highly appreciated thanks!Jorge A. NaranjoHPC Computational SpecialistNYU Abu DhabiOffice Tel (UAE): +971 2 628 4750Mobile (UAE): +971 56 319 2814New York University - Abu Dhabi (NYUAD) Saadiyat Campus - A2, Room-131 P.O. Box 129188Abu Dhabi, United Arab Emirateshttp://nyuad.nyu.eduPlease consider the environment before printing this email._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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problems compiling Freesurfer
by Jorge Naranjo 26 May '19

26 May '19

External Email - Use Caution Hi All, IM compiling freesurfer, after many bumps reached a point i havent figured out how to proceed. My setup: Centos7 GCC 4.8.5 Freesurfer 6.0.0 Dependencies as in /usr/pubsw/packages/ - KWWWidgets : CVS-vtk560 - petsc : 2.3.3-p13 - mni 1.5 - tcltktixblt : 8.4.6 - wxWidgets wxGTK-2.8.9 - xawplus: 3.1.0 Dependencies I built and installed in /usr/pubsw/packages/ - dcmtk: 3.6.4 - itk: 4.9.1 - vxl: v1.17.0 The rest of dependencies installed through RPM packages (yum) system-wise.. including VTK, etc ... then I do: FS_PACKAGES_DIR=/usr/pubsw/packages VTK_DIR=/usr VTK_LIBRARIES=/usr/lib64 PREFIX=/share/apps/NYUAD3/freesurfer/6.0.0 CMAKE_BUILD_TYPE=Release PETSC_DIR=/usr/pubsw/packages/petsc/current ITK_DIR=/usr/pubsw/packages/itk/4.9.1/lib/cmake/ITK-4.9/ OpenGL_GL_PREFERENCE=GLVND DANN_LIBRARIES=/usr/lib64 export CPATH=$CPATH:/usr/pubsw/packages/itk/4.9.1/include/ITK-4.9/ cmake3 ../freesurfer -DFS_PACKAGES_DIR=${FS_PACKAGES_DIR} -DVTK_LIBRARIES=${VTK_LIBRARIES} -DVTK_DIR=${VTK_DIR} -DCMAKE_INSTALL_PREFIX=${PREFIX} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -DPETSC_DIR=${PETSC_DIR} -DITK_DIR=${ITK_DIR} -DOpenGL_GL_PREFERENCE=${OpenGL_GL_PREFERENCE} -DANN_LIBRARIES=${DANN_LIBRARIES} -DUSE_PYTHON_INCLUDE_DIR=ON -DCMAKE_EXE_LINKER_FLAGS="-L/usr/lib64/ -lglut" make NOTE: the glut thing is because if I let the system use the libglut inside packages dir in the source code ... compilation breaks with : /bin/ld: ../packages/glut/libglut.a(glut_win.c.o): undefined reference to symbol 'glXCreateContextWithConfigSGIX' Well, the thing is that will all the above, the compilation breaks with this message: [ 57%] Built target trk_tools [ 57%] Built target streamlineFilter [ 57%] Built target testOrientationPlanesFromParcellation [ 57%] Building CXX object anatomicuts/CMakeFiles/dmri_match.dir/AnatomiCuts_correspondences.cxx.o /scratch/apps/singularity-sandboxes/braimcore-sandbox/SOFTWARE/FREESURFER/freesurfer/anatomicuts/AnatomiCuts_correspondences.cxx: In function ‘int main(int, char**)’: /scratch/apps/singularity-sandboxes/braimcore-sandbox/SOFTWARE/FREESURFER/freesurfer/anatomicuts/AnatomiCuts_correspondences.cxx:648:62: error: expected primary-expression before ‘double’ vcl_vector<unsigned int> assign = vnl_hungarian_algorithm<double>( distances ); //.GetAssignmentVector(); ^ make[2]: *** [anatomicuts/CMakeFiles/dmri_match.dir/AnatomiCuts_correspondences.cxx.o] Error 1 make[1]: *** [anatomicuts/CMakeFiles/dmri_match.dir/all] Error 2 make: *** [all] Error 2 Any help !?? will be highly appreciated thanks! *Jorge A. Naranjo* HPC Computational Specialist NYU Abu Dhabi Office Tel (UAE): +971 2 628 4750 Mobile (UAE): +971 56 319 2814 New York University - Abu Dhabi (NYUAD) Saadiyat Campus - A2, Room-131 P.O. Box 129188 Abu Dhabi, United Arab Emirates http://nyuad.nyu.edu Please consider the environment before printing this email.

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Visualizing Overlapping Areas in Significant Clusters
by Hua, Jessica 25 May '19

25 May '19

External Email - Use Caution Dear FreeSurfer Experts, I finished running my analyses, and FreeSurfer calculated the significant clusters for my contrasts (cache.th13.abs.sig.cluster.mgh). I am trying to show where significant clusters overlap between two different models. Do you know how I can create an ROI that only includes areas that overlap between different contrasts? Thank you! --- Jessica Hua, M.A.

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Checking number of parcels after transformation of an annotation file into a .nii.gz file
by Winkelbeiner, Stephanie A 24 May '19

24 May '19

External Email - Use Caution Hi Freesurfers, I'm struggling to find out if the number of parcels during a process of transformations from annot -> nii.gz has changed. I extended the parcels from 500.annot 2mm into the WM with mri_aparc2aseg \ --s s001 \ --annot 500.aparc \ --wmparc-dmax 2 \ --labelwm \ --hypo-as-wm \ --o mri/aparc.250+2mm.nii.gz and coregistered the resulting file to the DWI image using bbregister and mri_vol2vol. Using afni's probilistic tractography pipeline, I end up with more parcels than I thought I had. Is there a way to check the number of parcels after extension into the WM (mri_aparc2aseg)? I would be extremely grateful for some insight! Thanks, Stephanie The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

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TrackVis question
by Alan Francis 24 May '19

24 May '19

External Email - Use Caution Hi Ruopeng - I used Diffusion Toolkit to recon DTI data that was preprocessed using FSL. This data is from 7T scanners. I used an Angle threshold of 50. I tried various gradients from 6 - 120, but the images I am getting on trackvis are weird. I have attached a screenshot. Can you please shed some light on this? Thank you, Alan -- *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|* *Alan N. Francis PhDInstructor in PsychiatryHarvard Medical School* *Louis V. Gerstner III scholarMartinos Center for Biomedical Imaging* *Massachusetts General Hospital* *149, 13th street, Charlestown, MA* *alanf(a)bwh.harvard.edu <ezra_wegbreit(a)brown.edu> * *afrancis(a)mclean.harvard.edu <afrancis(a)mclean.harvard.edu>*

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question on surface analysis
by Barletta, Valeria 24 May '19

24 May '19

Dear Freesurfer, I have a surface file containing values of a cortical myelination index (rh.MS075_CME.mgh), and a lesion mask (rh.surf_CL03.mgh) What I need to do is: - Masking the surface file with the lesion mask, to create a new lesion mask that contains the myelination index values from rh.MS075_CME.mgh; - Assess the percentage (or also the absolute number) of vertices that are under a certain threshold of myelination index values whithin the new lesion mask. What is the best way to do this? Thank you, Vale

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XL defect in recon-all
by Barletta, Valeria 24 May '19

24 May '19

Dear Freesurfers, I tried to launch "recon-all -all" for an high-resolution 7T 0.75 isotropic MEMPRAGE, but the process got stuck on a XL defect in rh, numbered 54, measuring over 20,000 voxels!! How do I check, and eventually fix, this defect? Thank you, Vale

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Postdoctoral fellowships available in Toronto
by Rosanna Olsen 23 May '19

23 May '19

External Email - Use Caution The Rotman Research Institute at Baycrest (RRI) is seeking 9 outstanding postdoctoral fellows. A sub-set of the prospective fellows will be selected to be sponsored as the institutional candidates for a Banting Post-Doctoral Fellowship, and will work together with their prospective supervisors on the applications. [banting.fellowships-bourses.gc.ca <http://banting.fellowships-bourses.gc.ca/en/home-accueil.html>] The Rotman Research Institute (RRI) of Baycrest is a premier interdisciplinary, international centre for the study of human brain function. Our core research themes are: Cognitive Neuroscience, Aging and Brain Health, Alzheimer’s and Related Diseases, Computational Modeling and Neuroinformatics. Our research focuses on cognitive brain functions (including memory, executive function, attention, perception, and language), both in normal aging and in the presence of diseases and conditions that affect the brain, such as Alzheimer’s disease and other dementias, stroke, and traumatic brain injury. The Rotman Research Institute supports behavioral, neuropsychological, neuroimaging, and neurocomputational studies with state-of-the-art facilities, including eye-tracking, electroencephalography, and magnetoencephalography laboratories and a research-dedicated Siemens 3 Tesla MRI in-house at Baycrest. Rotman scientists who are currently recruiting post-doctoral fellows are: Jean Chen jchen(a)research.baycrest.org Brian Levine blevine(a)research.baycrest.org Randy McIntosh rmcintosh(a)research.baycrest.org Jed Meltzer jmeltzer(a)research.baycrest.org Morris Moscovitch momos(a)psych.utoronto.ca Rosanna Olsen rolsen(a)research.baycrest.org Jennifer Ryan jryan(a)research.baycrest.org Allison Sekuler vpr(a)research.baycrest.org and Eugenie Roudaia eroudaia(a)research.baycrest.org Stephen Strother sstrother(a)research.baycrest.org The postdoctoral fellows will conduct research on topics related to the areas of expertise of their prospective supervisors. In addition, fellowships at the RRI offer ample opportunities for collaborations both within the institute and with other researchers in Toronto. To find out more about recruiting scientists’ research areas, as well as a list of all scientists at the RRI, please follow individual links from here: https://www.baycrest.org/Baycrest/Research-Innovation/People/Researchers/Sc… Responsibilities and research opportunities may include but are not limited to: • Experimental design, data collection and analysis,manuscript preparation • Behavioural studies, including eyetracking • Structural neuroimaging with an emphasis on markers of learning-related changes • Multimodal functional neuroimaging, including fMRI, MEG, and/or EEG • Neurostimulation including tDCS, TMS • Data analysis using advanced, multivariate statistical tools applied to neuroimaging data Qualifications include but are not limited to: • Ph.D., M.D. or equivalent degree with an emphasis on neuropsychological theory • Experience in multivariate statistical techniques for data exploration, presentation, and analysis with advanced statistical software (e.g., R, MATLAB, Python) • Experience recruiting and testing research participants and patients • Experience with MRI, EEG, or MEG data collection and analysis The Banting Fellowships are open to Canadian citizens, Permanent Residents and Foreign Citizens. Starting dates are negotiable with the respective supervisors. To apply, please contact directly the scientist you wish to apply to, with a CV and cover letter, no later than *JUNE 10, 2019*. -- *Rosanna Olsen* Scientist, Rotman Research Institute *T* 416-785-2500, ext. 3509 rolsen(a)research.baycrest.org http://research.baycrest.org/rolsen *Baycrest Health Sciences* <http://www.baycrest.org/?utm_source=Signature&utm_medium=Email&utm_campaign…> 3560 Bathurst Street, Toronto, ON, M6A 2E1 Baycrest.org <http://www.baycrest.org/?utm_source=Signature&utm_medium=Email&utm_campaign…> | Facebook <http://www.facebook.com/baycrestcentre> | Twitter <http://www.twitter.com/baycrest> | LinkedIn <https://www.linkedin.com/company/baycrest> | YouTube <https://www.youtube.com/user/TheBaycrestChannel> | Instagram <http://instagram.com/baycrest>

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Hind's V1 Error for Freesurfer 6
by Lutz,Olivia (BIDMC - Psychiatry) 23 May '19

23 May '19

Dear Freesurfer group, We are interested in processing the Hind's V1 areas in addition to the Broadman areas. I am using a developmental verison of Freesurfer 6 from 1/18/2019 on Centos 6. I copied the V1_average into my $SUBJECTS_DIR folder and ran the following command on one subject (JS4501) as per the instructions the site https://surfer.nmr.mgh.harvard.edu/fswiki/BrodmannAreaMaps? >recon-all -s JS4501/ -label_v1 However, Freesurfer provides the following error: >ASSERTION FAILED: /local_mount/space/terrier/2/terrier_nightly_build/trunk/ah221-dev/utils/mrisurf_vals.c:4113 false ASSERTION FAILED: /local_mount/space/terrier/2/terrier_nightly_build/trunk/ah221-dev/utils/mrisurf_vals.c:4113 false /usr/local/freesurfer/bin/predict_v1.sh: line 123: 32339 Segmentation fault $cmd threshold_labelfile_at_0p8 /home/delta/Desktop/FREESURFER/BSNIP1/testing_V1/JS4501/label/rh.v1.prob.label /home/delta/Desktop/FREESURFER/BSNIP1/testing_V1/JS4501/label/rh.v1.predict.label thresholding the label...cat: /home/delta/Desktop/FREESURFER/BSNIP1/testing_V1/JS4501/label/rh.v1.prob.label: No such file or directory done @#@FSTIME 2019:05:22:13:08:17 predict_v1.sh N 3 e 831.12 S 0.41 U 831.05 P 100% M 256512 F 0 R 316437 W 0 c 332 w 20 I 0 O 8976 L 3.12 3.00 3.13 @#@FSLOADPOST 2019:05:22:13:22:08 predict_v1.sh N 3 1.75 1.91 2.39 Started at Wed May 22 12:55:23 EDT 2019 Ended at Wed May 22 13:22:08 EDT 2019 #@#%# recon-all-run-time-hours 0.446 recon-all -s JS4501 finished without error at Wed May 22 13:22:08 EDT 2019 done As a result, the rh.v1.predict.label & lh.v1.predict.label are generated but there are no v1.prob.labels. Is there anything I need to adjust to generate the Hind's V1 maps? Thanks! Olivia ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

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Re: [Freesurfer] recon-all exited ERRORS
by jennifer sorinas 23 May '19

23 May '19

External Email - Use Caution Dear Qiannan, I’m having the same problems, recon-all -all command is not working. FreeSurfer Developers help please! 😊 Best, Jennifer Enviado desde Correo<https://go.microsoft.com/fwlink/?LinkId=550986> para Windows 10

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Freesurfer May 2019