Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Results summary in QDEC
by Steve Petersen 08 Sep '20

08 Sep '20

External Email - Use Caution Dear Freesurfer experts, I performed group analysis in QDEC in order to compare cortical thickness between two groups using the Monte Carlo Z simulation correction. My question is, where is located the z-score of each significant cluster? Maybe in the second column named as Max?. Below you can find an example. In this case z-scores of the precuneus and the inferior parietal would be 3.422 and 3.926 respectively? Input /usr/local/freesurfer/subjects/qdec/Untitled/lh-Diff-HC-ad_plus-Intercept-thickness/sig.mgh # Frame Number 0 # srcsubj fsaverage # hemi lh # surface white # group_avg_surface_area 82220 # group_avg_vtxarea_loaded 1 # annot aparc # SUBJECTS_DIR /usr/local/freesurfer/subjects # SearchSpace_mm2 75146 # SearchSpace_vtx 146493 # Bonferroni 0 # Minimum Threshold 2.3 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold 0 mm^2 # CSD thresh 2.300000 # CSD nreps 10000 # CSD simtype null-z # CSD contrast NA # CSD confint 90.000000 # Overall max 4.16102 at vertex 61133 # Overall min -1.24867 at vertex 155746 # NClusters 2 # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs WghtVtx Annot 1 3.422 78695 820.44 -11.2 -54.8 49.4 0.00250 0.00190 0.00310 1664 4553.35 precuneus 2 3.926 52042 733.99 -30.8 -66.6 40.7 0.00410 0.00330 0.00490 1190 3620.13 inferiorparietal Simulation complete. Thanks in advance. Best regards, Steve.

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recon-all error
by Jie Zhao 08 Sep '20

08 Sep '20

External Email - Use Caution Dear freesurfer developer: I am using Freesurfer 7.1.1 and encounter an error like this when using recon-all : zhao@zhao-VirtualBox:~$ export SUBJECTS_DIR=/usr/local/freesurfer/subjects zhao@zhao-VirtualBox:~$ recon-all -s test4 -i sample-002.nii.gz -autorecon1 Subject Stamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 Current Stamp: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer Linux zhao-VirtualBox 4.15.0-20-generic #21-Ubuntu SMP Tue Apr 24 06:16:15 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Segmentation fault ERROR: Executable 'mri_ca_label -all-info failed! Is it missing from the distribution?' What can I do to fix this? Thanks Best regards Jie Zhao

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Piriform gyrus and other regions of the olfactory pathway
by Diógenes Bispo 08 Sep '20

08 Sep '20

External Email - Use Caution Dear, I would like to know how do I get thickness and cortical volume measurements of the piriform gyrus in Freesurfer version 7, as well as other regions of the olfactory pathway. Thanks. Diógenes Bispo Neuroradiologist diogenesdiego(a)gmail.com

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Re: [Freesurfer] Freeview not starting on Ubuntu 16.04: "failed to initialize XRandr"
by fsbuild 08 Sep '20

08 Sep '20

External Email - Use Caution Hi Alex, I see via a search for, ubuntu 16 Failed to initialize XRandr - that what you report happens when trying to connect remotely, e.g., via VNC, to something running X windows/graphics (for other flavors of linux as well).  This thread,https://serverfault.com/questions/788503/xrandr-error-when-accessing… seems to indicate the version of libGL.so could be an issue.  One take away is if you are trying do run X remotely, then you can test to see if a simple X program like glxgears can be run remotely (before trying to run freeview). I don’t think this one is much help as it reads like you already have these installed,https://askubuntu.com/questions/1039129/randr-extension-missing There could be interactions going on w.r.t what you have installed, and then having to set/configure some things so X can work remotely thru the google cloud.  I don’t know how/if Goggle cloud supports X forwarding etc., but I do know that other ways of doing cloud virtualization, e.g., thru docker containers, needs some work to run X applications remotely.   Maybe google cloud taking your virtual machine image and turning it into some kind of “container” to run (which can be done with docker I believe). If possible, I would first test the Ubuntu 16 virtual machine by running it directly on a local machine and check that glxgears and freeview work..  Then I would try running it in the cloud and see what happens with respect to trying to run those programs remotely.   If you don’t have to use Ubuntu 16, we have an Ubuntu 18 virtual disk image you can download and run that already has everything installed to run 7.1.0 (and you could update it to 7.1.1), https://drive.google.com/file/d/1bPvF9m2z4yRDIOv51B5bihU1VN_o2… - R. On Sep 7, 2020, at 14:22, Alex White <alexander.l.white(a)gmail.com> wrote:        External Email - Use Caution        Hi Thanks for the quit reply. I followed those instructions, it seemed that all those libraries were already installed. Freeview still won’t launch (even after rebooting). Here’s the output of the second command you suggested: alexlw@alexs:~$ sudo apt-get install libx11-dev  libxext-dev  libxrandr2  libxrender-devReading package lists... DoneBuilding dependency tree       Reading state information... Donelibxext-dev is already the newest version (2:1.3.3-1).libxext-dev set to manually installed.libxrandr2 is already the newest version (2:1.5.0-1).libxrender-dev is already the newest version (1:0.9.9-0ubuntu1).libxrender-dev set to manually installed.libx11-dev is already the newest version (2:1.6.3-1ubuntu2.2).The following packages were automatically installed and are no longer required:  guile-2.0-libs hdf5-helpers libaec-dev libavcodec-dev libavformat-dev  libavutil-dev libfontconfig1-dev libgc1c2 libgl2ps-dev libgsasl7  libhwloc-dev libibverbs-dev libjbig-dev libkyotocabinet16v5 libllvm5.0  liblzma-dev libmailutils4 libnetcdf-cxx-legacy-dev libntlm0 libnuma-dev  libopenjp2-7 libopenmpi-dev libswresample-dev libswscale-dev libtiffxx5  libxft-dev libxss-dev mailutils-common mpi-default-dev python3-boto tcl-dev  tcl8.6-dev tk-dev tk8.6-devUse 'sudo apt autoremove' to remove them.0 upgraded, 0 newly installed, 0 to remove and 41 not upgraded.Any other ideas? Thanks a million AlexOn Sep 7, 2020, at 12:21 AM, fsbuild <fsbuild(a)contbay.com> wrote:Hello Alex,I’m not sure Ubuntu 16.04 LTS has everything installed by default that the Qt graphics framework is looking to run in the X windows server.  You could try installing, $ sudo apt-get update$ sudo apt-get install libx11-dev  libxext-dev  libxrandr2  libxrender-dev- R.On Sep 7, 2020, at 01:52, Alex White <alexander.l.white(a)gmail.com> wrote:Qt: XKEYBOARD_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Fwd: Whole Thalamus Volume
by Al Qadi, Ameen 07 Sep '20

07 Sep '20

External Email - Use Caution ---------- Forwarded message --------- From: Al Qadi, Ameen <ameen.alqadi(a)icahn.mssm.edu> Date: Fri, Sep 4, 2020 at 6:09 PM Subject: Whole Thalamus Volume To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Dear Freesurfer Developers, I noticed a significant disparity in the left and right whole thalamus volumes between *aseg.stats *generated from recon-all and *ThalamicNuclei.v12.T1.volumes.txt *generated from the thalamic nuclei segmentation. Which set of volumes is the correct one to use? Best, Ameen -- Ameen Al Qadi MSBS Candidate Icahn School Of Medicine at Mount Sinai '20 +1-646-500-1521 ameen.alqadi(a)icahn.mssm.edu -- Ameen Al Qadi MSBS Candidate Icahn School Of Medicine at Mount Sinai '20 +1-646-500-1521 ameen.alqadi(a)icahn.mssm.edu

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Extracting hierarchical hippocampal segmentation volumes
by Kelsey Leigh Canada 07 Sep '20

07 Sep '20

External Email - Use Caution Hello, I am newer to Freesurfer and have been unable to find a reference on how to extract the volumes/voxels of the hierarchical segmentations using FS 7.1 (e.g, from rh.hippoAmygLabels-T1-T2.v21.CA.mgz). I am trying to compare manual segmentations to those generated by Freesurfer and the closest hierarchical segmentation is "CA". However, because the volume output (i.e., from quantifyHAsubregions.sh) does not seem specific to a given hierarchical segmentation, I am unsure how the molecular layer is being assigned for the "CA" segmentation given these voxels are assigned to the nearest voxel that isn't the molecular layer or background. Any guidance on how to extract volumes that reflect the "CA" segmentation would be greatly appreciated. Best regards, Kelsey Canada

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Re: [Freesurfer] Freeview not starting on Ubuntu 16.04: "failed to initialize XRandr"
by fsbuild 07 Sep '20

07 Sep '20

External Email - Use Caution Hello Alex, I’m not sure Ubuntu 16.04 LTS has everything installed by default that the Qt graphics framework is looking to run in the X windows server.   You could try installing,  $ sudo apt-get update$ sudo apt-get install libx11-dev  libxext-dev  libxrandr2  libxrender-dev - R. On Sep 7, 2020, at 01:52, Alex White <alexander.l.white(a)gmail.com> wrote:Qt: XKEYBOARD

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Freeview not starting on Ubuntu 16.04: "failed to initialize XRandr"
by Alex White 07 Sep '20

07 Sep '20

External Email - Use Caution Hello Freesurfer team, I installed the latest version of Freeview (from the file freesurfer-linux-centos7_x86_64-7.1.1.tar.gz) onto a Linux virtual machine on the google cloud platform. The machine is running Ubuntu 16.04.6 LTS. The installation seemed to go well but I can’t get Freeview to open. The command “freeview” yield this: QXcbConnection: Failed to initialize XRandr Qt: XKEYBOARD extension not present on the X server. Aborted (core dumped) I’ve searched online for ways to get the XKEYBOARD extension but couldn’t find a solution. Any advice? Thank you Alex White

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errors in the parcellation
by Mariana Vallejo Azar 04 Sep '20

04 Sep '20

External Email - Use Caution Dear When I visualize the parcellation of some subjects, I see some errors using Destrieux 2009 atlas: S Front Middle parcel furrow floods most of the homonymous gyrus. Lat Fis Vert is not identified correctly, among others errors. Is there any way to edit the parcellation? Best regards Cheers Mariana V.A (Argentina)

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mri_segstats quetsion
by Nasiriavanaki, Zahra 04 Sep '20

04 Sep '20

Dear Freesurferers Hi I am trying to extract the BOLD signal values from a functional subcortical area. I did the below steps to make the functional thalamus ROI and then used the mri_segstats to extract the BOLD signal from it. I would like to know 1-if my approach is correct? 2- should I use “lhthal3” as a mask? if so, what should I use as an input? 3-I see that the “mri_segstats” outputs one value for each voxel inside my ROI, is there a way to get one value across the whole ROI (lhthal3.nii.gz)? fslmaths 'aseg.nii.gz' -thr 10 -uthr 10 'lhthal.nii.gz' fslmaths 'lhthal.nii.gz' -mul 'sig.nii.gz' 'lhthal2.nii.gz' fslmaths 'lhthal2.nii.gz' -bin 'lhthal3.nii.gz' mri_segstats --seg aseg.nii.gz --i lhthal3.nii.gz --sfavg this.txt Thanks a lot M0na Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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