Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

eTIV and brainmask mismatch on Philips data
by Agnieszka Sabisz 30 May '19

30 May '19

External Email - Use Caution Hi all! We are running FS v.6.0. on a supercomputer operating on Linux. We have two sets of data - one from 1.5T Aera Siemens, second from 3.0T Achieva TX Philips. The T1 images on both scanners have comparable CNR, with an isotropic resolution of 1mm3 each. The recon-all finished with no errors, but in approximately half of the Philips data there is a significant (up to 40%) difference between the brain mask volume and eTIV (no such problem on Siemens). We inspected the Talairach registration (as is pointed that eTIV is calculated upon it) in the mismatched data with: tkregister2 --mgz --s <subject> --fstal --surf orig and in the corrupted data the brain mask and the WM-GM borders align in terms of placement but are of a wrong scale (proportionate to the "brainmask-to-eTIV" difference). What may be the reason and how to cope with that? We cannot normalize the volume data to eTIV (as it is not proper), what value should we use instead? Attached you will find example tkregister2 output screenshots. Best regards, Agnieszka Sabisz

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Mapping Electrode CT-Coordinates To FreeSurfer Space
by Adam Li 29 May '19

29 May '19

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to map CT-electrode-xyz coordinates to Freesurfer space. Now, there are two approaches: 1. Coregistering CT -> T1 MRI and then localizing contacts on the CT_in_T1 image volume 2. Localizing contacts in CT and then mapping those coordinates with the affine transformation Afterwards, I have a Nx3 matrix denoting the CT-xyz coordinates in the T1 image volume space. I usually run this with the T1.nii nifti image created from the raw .dicoms. However, my impression of the surfaces and overall Freesurfer analysis is that they are resampled into "Freesurfer space". The problem with this is then any sort of analysis to try to link the CT-xyz coordinates to any parcellation, or analysis done by FreeSurfer isn't correct (I am pretty sure). My end goal is to map these electrode coordinates to either: 1. White matter contact 2. Gray matter contact - mapped to an atlas label 3. Outside brain contact - if it lays outside the brain I am wondering how I can perform the NativeSpace -> FreeSurfer space mapping. I looked at the following: 1. https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat which explains how to convert surfaces/volumes/coords to Native Space, but I want to do the reverse. It seems that it is possible for me to just map all the surfaces, volumes, etc. of interest into native space, but that seems like a lot of extra work compared to doing what I am proposing. Any comments on the pros/cons of either approach would also be helpful! I've searched the list and no one has had a detailed similar problem. Does anyone have any thoughts on how to go about this and can also possibly provide a link to more information that can explain things further? Thank you! Best Regards, Adam Li PhD Student in Biomedical Engineering Johns Hopkins University & School of Medicine

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Bad segmentation in gadolinium MRI
by María Martínez Rodrigo 29 May '19

29 May '19

External Email - Use Caution Dear all, Some of my images have been taken in patients with gadolinium, so some regions are highlighted because of the contrast effect. The problem is that, in many cases, this produces a bad parcelation of the brain. For instance, in the example you will find attached, the insula is smaller than it should be (parcels blue, dark read and yellow must be included in the insula). Is there any way to avoid this effect or to correct these high intensities without using manually correction? Thanks in advance, Maria.

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No module named 'freesurfer.algorithm'
by Kelly Vaughn 29 May '19

29 May '19

External Email - Use Caution Hello FreeSurfer Community, Does anyone have any advice on diagnosing/solving the following error: Traceback (most recent call last): File "/usr/local/freesurfer/bin/mri_label_fusion", line 11, in <module> from freesurfer.algorithm import maxflow, performFrontPropagation3D ModuleNotFoundError: No module named 'freesurfer.algorithm' set: No match. I am using infant FreeSurfer, so it is possible that this error is specific to that. I've searched through the FreeSurfer listservs and can't find any mention of this error. I am using the stable release of FreeSurfer: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz <https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Lin…> on RHEL 7. Please let me know if you have any suggestions on what is causing this error or how to solve it. If it looks specific to infant FreeSurfer, I will contact those developers. Thank you, Kelly Vaughn -- Kelly Vaughn, Ph.D. Postdoctoral Research Fellow Children's Learning Institute

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Some questions about mris_make_template and downsample
by Jingyue Zhang 29 May '19

29 May '19

External Email - Use Caution Dear Freesurfer experts: Hello! I'm a new student to surface based fMRI analysis. Now I'm dealing with a functional parcellation problem. The subjects in my dataset has different vertex number and I need to do a group level parcellation, so I decided to make a group reference template. My step is almost following this post: https://www.mail-archive.com/freesurfer@surfer.nmr.mgh.harvard.edu/msg00420… ,the lh.wholebrain.tif and lh.sphere.reg for two test subjects have successfully generated. But I'm still wondering about these files and what to do next to get my individual fMRI time series on vertex registerd to the template. The second question is, the vertex number (~100000) is much more than my voxel based masked data (~50000). Neither is easy to do the susequent analysis efficiently. So how should I correctly downsample it? Should I downsample the template or downsample my surface before making template? Will mris_decimate work? The last question is my subject has gifti format sulc and curv data (.shape.gii). I have tried to use MRI_read and MRI_write to write to an .mgh file and add -sulc sulc.mgh for each command and they seems worked. Can I convert them to file like .sulc? Or just keep the .mgh and -sulc sulc.mgh is OK? I'm looking forward to hear your reply! Really thanks for your help! Best wishes, Jingyue Zhang

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longitudinal subfields exited with ERRORS
by Jaime Gomez 29 May '19

29 May '19

External Email - Use Caution Hello FreeSurfer Developers, I'm trying to run segmentHA_T1_long.sh ERROR: MATLAB is exiting because of fatal error /Applications/freesurfer/bin/run_SegmentSubfieldsT1Longitudinal.sh: line 37: 49858 Killed: 9 "${exe_dir}"/SegmentSubfieldsT1Longitudinal.app/Contents/MacOS/SegmentSubfieldsT1Longitudinal $args Darwin jaimes-Mac-Pro.local 18.2.0 Darwin Kernel Version 18.2.0: Fri Oct 5 19:41:49 PDT 2018; root:xnu-4903.221.2~2/RELEASE_X86_64 x86_64 longitudinal subfields exited with ERRORS at Tue May 28 17:53:02 CEST 2019 I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) freesurfer-darwin-OSX-ElCapitan-dev-20190328-6241d26 2) Platform: macOS 10.14.1 (18B75) 3) Darwin jaimes-Mac-Pro.local 18.2.0 Darwin Kernel Version 18.2.0: Fri Oct 5 19:41:49 PDT 2018; root:xnu-4903.221.2~2/RELEASE_X86_64 x86_64:16 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux 4) long-hippocampal-subfields-T1.log: see attached

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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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