Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30081 discussions

Error with mri_glmfit command
by Martin Juneja 30 May '19

30 May '19

External Email - Use Caution Hi FS experts, I want to find clusters showing an association between cortical measures and behavior x6 (sex, age and variables x1-x5 as covariates). My FSGD file looks like: GroupDescriptorFile 1 Class Male Class Female Variables x1 x2 x3 x4 x5 x6 Age Input S001 Male 120 103 109 124 113 94 113 36 Input S003 Male 91 101 86 103 109 95 96 29 Input S004 Male 104 116 110 96 115 108 112 39 Input S005 Female 116 114 103 127 115 106 118 32 Input S006 Female 93 100 90 100 117 90 97 23 Input S008 Male 70 80 80 66 78 83 71 40 Input S009 Female 125 114 115 125 118 104 124 45 Input S010 Female 96 91 93 101 91 92 94 42 Input S011 Male 104 92 97 111 84 103 98 45 Input S012 Female 79 81 90 74 82 80 78 22 Input S014 Male 120 94 118 114 105 87 107 44 Input S015 Female 94 86 92 100 80 93 88 29 Input S016 Male 98 92 107 88 95 90 95 33 Input S017 Female 96 100 112 83 95 104 99 21 Input S018 Male 98 93 96 103 104 87 96 42 Input S019 Female 105 120 99 110 113 114 114 26 Input S020 Female 105 107 104 103 113 100 109 27 Input S022 Female 116 98 115 111 111 89 109 25 Input S023 Female 98 91 94 105 86 96 94 21 Input S024 Male 116 101 119 105 90 112 111 43 Input S025 Female 143 102 134 129 110 95 120 21 Input S028 Female 72 80 77 71 82 78 71 41 Input S029 Male 104 100 116 92 94 105 104 25 Input S030 Female 120 96 115 116 103 92 109 18 Input S031 Female 114 103 111 111 99 105 112 29 Input S033 Male 121 99 108 127 104 96 111 20 Input S035 Male 112 104 104 115 103 103 110 20 Input S036 Female 111 103 103 113 106 98 109 28 Input S037 Male 108 91 108 103 92 91 99 30 Input S038 Male 103 99 102 102 117 89 103 18 Input S039 Male 106 114 116 94 112 107 112 21 Input S040 Male 99 98 97 102 94 100 99 41 Input S041 Male 103 109 97 109 110 103 109 26 My contrast file looks like: 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 0 0 After I run mri_glmfit command, I get following error: ERROR: matrix is ill-conditioned or badly scaled, condno = 385372 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. I would really appreciate any help in figuring out this issue. Thanks, MJ

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QA_tools citation
by Nasiriavanaki, Zahra 30 May '19

30 May '19

Dear Freesurfer experts Hi I was wondering how should I cite the Freesurfer QA_tools in a paper. I couldn’t find any references in the web page (https://surfer.nmr.mgh.harvard.edu/fswiki/QATools) Thanks Mona

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Postdoc in developmental neuroimaging
by Signe Bray 30 May '19

30 May '19

External Email - Use Caution The Department of Radiology and the Child and Adolescent Imaging Research (CAIR) Program at the University of Calgary are seeking applications for a post-doctoral scholar in developmental neuroimaging. The postdoc will work with the Bray Neuroimaging Lab led by Dr. Signe Bray (@braynimaginglab, http://brayneuroimaginglab.ca) on studies of healthy brain development and neurodevelopmental conditions such as autism and preterm birth. Applicants should have a background in psychology, neurosciences, biomedical engineering or a relevant discipline. Experience with neuroimaging and/or pediatric research and strong data analytic skills is required as well as interest in computational modeling and novel approaches to neuroimaging analyses. This is a 2-year position with the possibility of extension. Applicants should submit a letter of interest and CV to slbray(a)ucalgary.ca. On-site meetings at OHBM can be scheduled. The CAIR Program is a pediatric dedicated imaging program based at the Alberta Children’s Hospital that manages a research-dedicated 3T MR scanner, MRI-compatible EEG system, eye tracking and MRI simulator for preparing children. Calgary is less than an hour’s drive from the majestic Rocky Mountains and offers outstanding opportunities for outdoor recreation including world class skiing, hiking and climbing. The city has been named a cultural capital of Canada and one of the best places to live in the world, Calgary is a city of leaders – in business, community, philanthropy and volunteerism boasts the most extensive urban pathway and bikeway network in North America.

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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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