Freesurfer June 2020

freesurfer@nmr.mgh.harvard.edu

91 participants
130 discussions

MGN and LGN in ThalamicNuclei segmentation
by julienbesle 17 Jun '20

17 Jun '20

External Email - Use Caution Hello, I'm interested in locating the MGN and LGN using segmentationThalamicNuclei, but there is a mismatch between their location in the discrete segmentation (ThalamicNuclei.v10.T1.mgz) and the underlying probability maps obtained by setting environment variable WRITE_POSTERIORS to 1. While the LGN in the segmentation has many voxels within the corresponding area of maximum probability, many high-probability voxels are missing from it. For the MGN, the segmentation volume is restricted to a small number of voxels in the most lateral/posterior/superior part of the area of max probability, but most high-probability voxels are absent from the segmentation. Any reason why this could be happening? Is there anything I can do (parameters I can change in the script) to fix this? The defaut Freesurfer segmentation ("thalamus proper") is generally larger than the segmentation output by segmentThalamicNuclei, except in the area of the LGN, where the thalamic segmentation extends more laterally/inferiorly, as if it had been extended in order to include the LGN (although imperfectly). Unfortunately, this does not seem to be the case for the MGN (which is my primary area of interest). To solve the issue, I'm thresholding the posterior probability maps at p>0.2 for both LGN and MGN and adding these voxels to the discrete segmentation, but that's not very satisfactory. Actually, it wasn't very clear to me from the published paper how the discrete segmentation is obtained from the posterior probability maps and if any cut-off value is used to decide whether to include any voxel in the final discrete segmentation? (Note that I'm using T1-weighted MPRAGE data at a resolution of 0.7 mm isotropic) Thanks Julien

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"unknown" voxels in medial temporal lobe aparc+aseg
by Caspar M. Schwiedrzik 16 Jun '20

16 Jun '20

External Email - Use Caution Hi! We are facing some issues in the aparc+aseg of the medial temporal lobe. As you can see on the image, there are quite a few voxels labeled as unknown in both hemispheres, and generally, there seems to be a bit of a mess in that general area in the aparc+aseg (above), while everything is marked as cortex in aseg (below). We see this pattern in a few subjects. Is there a way to get these voxels assigned to a structure? wm edits have not fixed the issue so far. Thank you! Caspar [image: aparc.png]

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extracting clusters for each timepoints for longitudinal analyses
by miracle ozzoude 16 Jun '20

16 Jun '20

External Email - Use Caution Hello, I ran a pet longitudinal paired t-test analysis with 2 timepoints using mri_glmfit and I found significant clusters. I want to extract the values of these significant clusters for each timepoints. How do I go about doing this? Thank you. Best, Paul.

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Splitting surface overlay into separate files
by Mason Wells 16 Jun '20

16 Jun '20

External Email - Use Caution Hi Experts, Apologies if this is a rather simple question. Is there a FreeSurfer equivalent of fslmaths? I have an atlas overlay that has 25 visual areas in a single .mgz file. I want to separate each atlas region into a different file, so that I end up with 25 surface atlas regions. Is there a command that could achieve this? My next question is whether or not there is a Freesurface command that can be used to complete surface based correlations. For example, if I want to check for the overlap between two ROIs. I have been using fslcc to do this in the volume, but perhaps freesurfer has something similar to do this on the surface? Cheers, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628

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mri_glmfit-sim running for 4 days and still not finished
by Mageshwar Selvakumar 16 Jun '20

16 Jun '20

External Email - Use Caution Dear freesurfer community, I have been working with the freesurfer stat files for some time now but never got to explore the group analysis pipeline. I tried this mri_glmfit command to see the correlation of my anatomical data(57 subjects) with a clinical measure. The uncorrected version ran well (took a couple of minutes)and I was able to view it on freeview. I tried to run the mri_glmfit-sim command with the same settings as in freesurfer webpage, with just a modification to use 6 cores instead on 1, and saw the comment that it takes around 20 minutes but this one has been running for me for the last four days. I'm not sure what is going wrong. Can someone please guide me through and let me know what kind of information I can pass on here, so that you can help me out. Thank you, Kind regards Mageshwar Selvakumar, M.Sc Department of Pharmakologische Bildgebung und Bildanalyse Friedrich Alexander Universität Erlangen Nürnberg Office: Fahrstr. 17, 91054 Erlangen Phone: + 49-9131-8522898

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mri_glmfit error
by 邓刊 16 Jun '20

16 Jun '20

External Email - Use Caution Hello Freesurfer Experts! I met the mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08.I am trying to run a 8 group 3 variables analysis: with diagnosis being my variable of interest and trying to regress out the effects of gender,background,age,education and seizure. 1. Command line: mris_preproc --fsgd qdec/group.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.thickness.fwhm10.groups.mgh mri_glmfit --y lh.thickness.fwhm10.groups.mgh --fsgd group.fsgd dods --C Difference.group.mtx --surf fsaverage lh --cortex --glmdir fwhm10.thickness.glmdir 2. The FSGD file (see attached) 3. And the design matrix: 1 1 1 1 -1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 (or see attached) I encounter this error. I have no idea how to proceed.Is all this because I have too many covariates? I am looking forward to your response! Thanks, Kan

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Re-register functional volume rotation issue
by Paul Soulos 15 Jun '20

15 Jun '20

External Email - Use Caution Hello, I am trying to solve an issue with reregistering functional images onto a new anatomical. Let’s say I have two anatomical images from sub01-ses01/orig.mgz and sub01-ses02/orig.mgz, as well as functional files each registered to their corresponding anatomical sub01-ses01/fmcpr.nii.gz and sub01-ses02/fmcpr.nii.gz. My goal is to reregister Dsub01-ses01/fmcpr.nii.gz onto the sub01-ses02 anatomical. Screenshots of my issue are available at: https://imgur.com/a/9GDm9yp To create a mapping between the two anatomical images, I first run: $ mri_cvs_register --mov sub01-ses01 --template sub-01-ses-02 When I view the output of the mri_cvs_register command, everything is lined up and looks good: https://i.imgur.com/SvjPVHX.png Next, I reregister sub01-ses01/fmcpr.nii.gz using the mapping created with mri_cvs_register: $ mri_vol2vol --noDefM3zPath --mov sub01-ses01/fmcpr.nii.gz --m3z $SUBECTS/sub01-ses01/cvs/final_CVSmorph_to-sub01-ses02.m3z --o sub01-ses01/fmcpr.ses02space.nii.gz --nearest --targ sub01-ses02/orig.mgz When I view sub01-ses01/fmcpr.ses02space.nii.gz over sub01-ses02/orig.mgz, the functional image is off by 90 degrees. This is unexpected: https://i.imgur.com/CpGtKyM.png If I manually rotate the functional image in Freeview by 90 degrees, it looks good: https://i.imgur.com/SkDNzuK.png mri_vol2vol has a --rot argument, so I tried to use this to perform the rotation automatically. Rather than 90 degrees, I now have to specify -90 degrees. Unfortunately, the output when I specify the rotation in mri_vol2vol does not line up well with the anatomical. https://i.imgur.com/vjxV6rv.png Does anyone know why this is happening? Please let me know if you have any suggestions. Thank you! Paul

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BIDS Common Derivatives released
by Franklin Feingold 15 Jun '20

15 Jun '20

External Email - Use Caution Hello! The BIDS community is proud to announce the release of Common Derivatives! Derivatives are the outputs of preprocessing pipelines, capturing data and meta-data sufficient for a researcher to understand and (critically) reuse those outputs in subsequent pipelines. This specification can be found at: https://bids-specification.readthedocs.io/en/stable/05-derivatives/01-intro… Common principles for derivative datasets: * Derivative datasets describe the contents of the dataset, the methods by which it was generated, and the original dataset(s) that were used to generate it. This metadata is mandatory at the dataset level and optional at the file level. * Derivative files must be distinguishable from raw files. A generic description (desc-) entity allows this if no other entity applies. * The spatial interpretation of data, if applicable, can be specified with a space entity and SpatialReference metadata. Releasing the common principles for derivative datasets will enable further progress into our modality specific derivative initiatives such as, electrophysiological<https://github.com/bids-standard/bep021>, PET, and diffusion MRI<https://github.com/bids-standard/bids-bep016>. Our immediate attention will shift to focus on specifying anatomical and functional derivatives (Look out for the pull requests soon!). BEP 028: (provenance)<https://github.com/bids-standard/bids-specification/pull/487> is a closely related effort that we hope to see progress quickly as well! We would like to thank our incredible community of contributors and members that helped push this extension over the finish line! Thank you, Chris and Franklin - BIDS Maintainers

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Re: [Freesurfer] Freeview on Mac not starting due PETSC error {Disarmed}
by fsbuild 15 Jun '20

15 Jun '20

External Email - Use Caution Hello Alex, Did you try the install with the 7.1.0 release using the .pkg file installer from https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.0/free… If you did not go thru all the security exemptions (not related to your firewall settings) on Catalina, then something may be blocked from running.  The install procedure to follow using the .pkg installer is under,https://surfer.nmr.mgh.harvard.edu/fswiki//FS7_mac I did this on my mac running Catalina and had no issues running freeview. - R.. On Jun 14, 2020, at 17:45, Alex White <alexander.l.white(a)gmail.com> wrote:        External Email - Use Caution        Hi Ruopeng I tried deleting that .plist file, but it did not work, even after restarting the machine. The same PETSC crash occurred when I try to start Freeview either through the terminal or clicking on the icon. Thanks for your continued help, AlexOn Jun 14, 2020, at 2:29 PM, Wang, Ruopeng <RWANG4(a)mgh.harvard.edu> wrote:Can you delete this file and wait for a minute and then try starting freeview again?/Users/USERNAME/Library/Preferences/edu.harvard.mgh.nmr.FreeView.plistReplace USERNAME with your actual username. On Jun 14, 2020, at 1:47 PM, Alex White <alexander.l.white(a)gmail.com> wrote:        External Email - Use Caution        Hello Ruopeng, Thanks for the quick reply! I tried launching Freeview by double-clicking on the app icon, and I tried installing the latest build. The same crash occurs (full output copied again below. Also, I do have XQuartz 2.7.11 and it can run xeyes. And yes, FREESURFER_HOME and SetUpFreesurfer.sh both reference the current version 7.1.0. I didn’t see any LD_LIBRARY_PATH in my shell init file. Here’s what’s in my .bashrc file: % cat .bashrc#set freesurfer directories and set up scriptexport FREESURFER_HOME=/Applications/freesurfer/7.1.0export SUBJECTS_DIR=$FREESURFER_HOME/subjectssource $FREESURFER_HOME/SetUpFreeSurfer.shAny other ideas? Thanks, AlexCrash output:  ~ % freeview[0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger[0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshootin…: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash.[0]PETSC ERROR: --------------------- Error Message ------------------------------------[0]PETSC ERROR: Signal received![0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 16, Tue Sep 23 10:02:49 CDT 2008 HG revision: 31306062cd1a6f6a2496fccb4878f485c9b91760[0]PETSC ERROR: See docs/changes/index.html for recent updates.[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.[0]PETSC ERROR: See docs/index.html for manual pages.[0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: Unknown Name on a darwin15. named gse7359200.local by alexlw Sun Jun 14 10:46:00 2020[0]PETSC ERROR: Libraries linked from /autofs/cluster/pubsw/arch/MacOS10.11/packages/petsc/2.3.3/src/petsc/lib/darwin15.6.0-c-opt[0]PETSC ERROR: Configure run at Mon Apr 22 13:14:02 2019[0]PETSC ERROR: Configure options --with-debugging=no --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3[0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file[unset]: aborting job:application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0On Jun 14, 2020, at 6:56 AM, Wang, Ruopeng <RWANG4(a)mgh.harvard.edu> wrote:HI Alex,Have you tried launching freeview by double-clicking freeview.app bundle? Can you also try the latest build from here?https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeviewBest,RuopengOn Jun 14, 2020, at 12:07 AM, Alex White <alexander.l.white(a)gmail.com> wrote:        External Email - Use Caution        Hello freesurfer team! I can’t get Freeview to start up on my Mac (Catalina v 10.15.15). It worked intermittently earlier this year, then stopped working. I updated Freeview, and then all of freesurfer, and still have the same problem. So now I have this version of freesurfer:  freesurfer-darwin-macOS-7.1.0-20200511-813297bTyping “freeview” into the terminal generates the following error: [0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger[0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshootin…: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash.[0]PETSC ERROR: --------------------- Error Message ------------------------------------[0]PETSC ERROR: Signal received![0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 16, Tue Sep 23 10:02:49 CDT 2008 HG revision: 31306062cd1a6f6a2496fccb4878f485c9b91760[0]PETSC ERROR: See docs/changes/index.html for recent updates.[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.[0]PETSC ERROR: See docs/index.html for manual pages.[0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: Unknown Name on a darwin15. named gse7359200.local by alexlw Sat Jun 13 20:58:43 2020[0]PETSC ERROR: Libraries linked from /autofs/cluster/pubsw/arch/MacOS10.11/packages/petsc/2..3.3/src/petsc/lib/darwin15.6.0-c-opt[0]PETSC ERROR: Configure run at Mon Apr 22 13:14:02 2019[0]PETSC ERROR: Configure options --with-debugging=no --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3[0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file[unset]: aborting job:application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0I searched through the log of previous emails and found several others with “PETSC errors” but could not discern a common solution. Help? Thank you, Alex White PS: I also can’t get Freeview to launch on a linux machine, and will send a report on that in a separate email. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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recon-all hanging, how to examine defect
by KennethSPrice 15 Jun '20

15 Jun '20

External Email - Use Caution Hello freesurfers, I am running recon-all on one of my subjects and it is hanging on a defect. How do I examine the reason it is hanging? Freeview the defect? Any help would be appreciated. Thanks, Ken Sent with [ProtonMail](https://protonmail.com) Secure Email.

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Freesurfer June 2020