Freesurfer September 2017

freesurfer@nmr.mgh.harvard.edu

109 participants
199 discussions

PySurfer 0.8.0 release
by Eric Larson 26 Sep '17

26 Sep '17

Dear All, We are pleased to announce the 0.8.0 release of PySurfer, a Python-based package for visualizing Freesurfer data. This release includes bugfixes and multiple enhancements, including: - The surface geometry that is displayed can now be changed after initializing a Brain instance with e.g. brain.set_surf("smoothwm"). - Allow using custom matplotlib colormap objects or the names of custom colormaps that have been registered with matplotlib. - Added four new colormaps from seaborn: rocket, mako, icefire, and vlag. - Terrain interaction is now possible via the ``interaction`` keyword argument. - An API reference page is now available. - Support is now provided for visualizing vector-valued (3 values per vertex) data. Please see our website (http://pysurfer.github.io/) for information on installation, documentation, and the example gallery. We hope you find it useful in your research! Eric Larson, Michael Waskom, Alexandre Gramfort, and the Nipy team

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modeling thickness data at a given age
by Eryilmaz, H. Hamdi 26 Sep '17

26 Sep '17

Dear all, We are modeling changes in cortical thickness over time using a cross-sectional design. We have two groups of participants, age 8 to 18. In the cortical regions that interest us, there is generally a linear decline in thickness with age. Each group can be fitted to a best-fit line. The question we are interested in is whether there is a significant difference in thickness between groups at a given age (i.e., not just collapsed across age) — specifically, at the earliest age point (age=8). Is this possible to model across the brain surface in Freesurfer? Thanks, Hamdi and Josh

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Volume Version of ?h.sphere.reg and method to read it
by Daniel van de Velden 26 Sep '17

26 Sep '17

Dear Freesurfer Team, I am using your reconstruction pipeline for my study. Since I need to morph all my subjects to an average subject (using mne-python for this) for upcoming a Volume Source Analysis I deeply looked into the whole source-code of both software packages. Narowing down the problem, I think I will need a volume version of the ?h-sphere.reg files, which are created during the whole reconstruction process. Mne-python reads the subject specific 'sphere_tris' from this file. If I would have a similiar file for the volume edges that would be helpful. Do you agree with my conclusion and see where I am going? Thanks in advance for any kind of help. Yours sincerely, Daniel van de Velden .

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mne_surf2bem error persists after editing file in freeview
by Anna Kasdan 25 Sep '17

25 Sep '17

I am trying to create a high-resolution image to use with mne in mne_analyze. I first ran mkheadsurf -subjid s and this did not result in any errors. I then ran mne_surf2bem --surf ../surf/lh.seghead --id 4 --check --fif s-head.fif and ran into an error about vertices for a few of my subjects. input file # 1 : ../surf/lh.seghead / id = 4 / sigma N/A output file : EVO07-head.fif New quad file : nvert = 288077 nquad = 294014 Triangle and vertex normals and neighboring triangles...[done] Vertex neighbors...Too many neighbors for vertex 92055. I tried editing the seghead.mgz file in freeview, and filled in the voxels that were missing at the neck. I then reran the mkheadusrf command (mkheadusrf -subjid s --noseghead), still with no errors, but got the same error as before again when I ran the mne_surf2bem command. Suggestions? Many thanks! Anna

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longtitudinal pipeline
by miracle ozzoude 25 Sep '17

25 Sep '17

Hello Freesurfer, For the longitudinal pipeline, the website/ recon-all -help suggested that I calculate the different on the results from the longitudinal command (e.g. tp2.long.longbase - tp1.long.longbase). Let say, my timepoints were named 0001a.long.0001.longbase and 0001b.long.0001.longbase. is there a command i can use to preform this? Second question, i want to extract the output of the longitudinal pipeline using asegstats2table and aparcstats2table commands. what flag/s should i include in the original command to perform this? Thanks. Paul

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Re: [Freesurfer] Error in segmentHA_T1
by Iglesias Gonzalez, Eugenio 25 Sep '17

25 Sep '17

Dear Tiril, Were you pointed to downloading a version of Java when you first tried to run the subfields? If so, did you follow the instructions? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Tiril Pedersen Gurholt <t.p.gurholt(a)medisin.uio.no> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, 22 September 2017 at 20:47 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Error in segmentHA_T1 Dear Experts, I recently installed Freesurfer development version (dated Sept. 16, 2017) on a Mac Sierra (10.12.6). When trying to run segmentHA_T1.sh I encounter a java problem: "JavaVM: Failed to load JVM: /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bundle/Libraries/libserver.dylib». See full error message below. The java.opts file in MCRv80/bin/maci64 is dated Nov. 5, 2014. There also appears to be a problem with a Matlab app (?), although matlab runtime has been installed. Any ideas as to how to fix these problems? Best regards, Tiril Error message: #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Fri Sep 22 20:17:14 CEST 2017 ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer/MCRv80//runtime/maci64:/Applications/freesurfer/MCRv80//bin/maci64:/Applications/freesurfer/MCRv80//sys/os/maci64: Warning: application is running on a locale different from the original platform locale. JavaVM: Failed to load JVM: /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bundle/Libraries/libserver.dylib JavaVM FATAL: Failed to load the jvm library. 2017-09-22 20:17:16.597 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.599 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.599 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.600 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.600 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.601 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.601 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.602 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.602 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. JavaVM: Failed to load JVM: /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bundle/Libraries/libserver.dylib JavaVM FATAL: Failed to load the jvm library. Fatal Error on startup: Unable to start the JVM because of a bad Java option or unknown error. Please check your java.opts file. #-------------------------------------------- #@# Hippocampal Subfields processing (T1) right Fri Sep 22 20:17:16 CEST 2017 ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer/MCRv80//runtime/maci64:/Applications/freesurfer/MCRv80//bin/maci64:/Applications/freesurfer/MCRv80//sys/os/maci64: Warning: application is running on a locale different from the original platform locale. JavaVM: Failed to load JVM: /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bundle/Libraries/libserver.dylib JavaVM FATAL: Failed to load the jvm library. 2017-09-22 20:17:18.151 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.151 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.152 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.152 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.153 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.153 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.153 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.154 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.154 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. JavaVM: Failed to load JVM: /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bundle/Libraries/libserver.dylib JavaVM FATAL: Failed to load the jvm library. Fatal Error on startup: Unable to start the JVM because of a bad Java option or unknown error. Please check your java.opts file.

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Brain.finalsurfs.mgz output
by Fereshte 24 Sep '17

24 Sep '17

Dear Experts, What is "brain.finalsurfs.mgz" file? I mean it is the output of which stage in recon-all pipeline? I couldn't find any information about this output on the site. Thank you. Cheers

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Hemisphere white surface
by Fereshte 24 Sep '17

24 Sep '17

Dear Experts, I have run the autorecon2 without errors but i can't see rh.white and rh.white outputs ( lh.white.K and lh.white.H instead). Could you please help? Thank you

2 2

bad midline cut
by Gabor Perlaki 23 Sep '17

23 Sep '17

I've a subject, where the midline cut is bad (see the attached pictures), therefore the segmented left lateral ventricle also includes considerable number of voxels from the right one. Is it possible to correct it somehow?

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Error in segmentHA_T1
by Tiril Pedersen Gurholt 22 Sep '17

22 Sep '17

Dear Experts, I recently installed Freesurfer development version (dated Sept. 16, 2017) on a Mac Sierra (10.12.6). When trying to run segmentHA_T1.sh I encounter a java problem: "JavaVM: Failed to load JVM: /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bundle/Libraries/libserver.dylib». See full error message below. The java.opts file in MCRv80/bin/maci64 is dated Nov. 5, 2014. There also appears to be a problem with a Matlab app (?), although matlab runtime has been installed. Any ideas as to how to fix these problems? Best regards, Tiril Error message: #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Fri Sep 22 20:17:14 CEST 2017 ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer/MCRv80//runtime/maci64:/Applications/freesurfer/MCRv80//bin/maci64:/Applications/freesurfer/MCRv80//sys/os/maci64: Warning: application is running on a locale different from the original platform locale. JavaVM: Failed to load JVM: /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bundle/Libraries/libserver.dylib JavaVM FATAL: Failed to load the jvm library. 2017-09-22 20:17:16.597 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.599 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.599 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.600 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.600 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.601 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.601 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.602 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.602 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. JavaVM: Failed to load JVM: /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bundle/Libraries/libserver.dylib JavaVM FATAL: Failed to load the jvm library. Fatal Error on startup: Unable to start the JVM because of a bad Java option or unknown error. Please check your java.opts file. #-------------------------------------------- #@# Hippocampal Subfields processing (T1) right Fri Sep 22 20:17:16 CEST 2017 ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer/MCRv80//runtime/maci64:/Applications/freesurfer/MCRv80//bin/maci64:/Applications/freesurfer/MCRv80//sys/os/maci64: Warning: application is running on a locale different from the original platform locale. JavaVM: Failed to load JVM: /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bundle/Libraries/libserver.dylib JavaVM FATAL: Failed to load the jvm library. 2017-09-22 20:17:18.151 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.151 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.152 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.152 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.153 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.153 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.153 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.154 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.154 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. JavaVM: Failed to load JVM: /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bundle/Libraries/libserver.dylib JavaVM FATAL: Failed to load the jvm library. Fatal Error on startup: Unable to start the JVM because of a bad Java option or unknown error. Please check your java.opts file.

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Freesurfer September 2017