Freesurfer October 2023

freesurfer@nmr.mgh.harvard.edu

69 participants
95 discussions

TRACULA Error: Subregion Segmentation aparc+aseg+thalnuc.nii.gz
by Lauren Stephens 31 Oct '23

31 Oct '23

External Email - Use Caution Hi FreeSurfers, I am trying to troubleshoot an error during TRACULA preprocessing and the issue seems related to the creation of aparc+aseg+thalnuc.nii.gz. The subregion segmentation prior to trac-all -prep was successful and mri/ThalamicNuclei.v13.T1.FSvoxelSpace.mgz and other Thalamic Nuclei files were generated. In the archives I saw two others have experienced a similar issue without a resolution in the thread. I am using FreeSurfer 7.3.2 on an iMac Pro with Ventura 13.6. I have attached the log file, log error, and my configuration file. Any help would be greatly appreciated! Thank you, Lauren Stephens Lauren Stephens, MS Assistant Clinical Research Coordinator Department of Psychiatry and Behavioral Science Stanford University School of Medicine E: laurenss(a)stanford.edu P: (650)-725-1716

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Using Synthseg segmentations to fix recon-all outputs
by Maya Yablonski 31 Oct '23

31 Oct '23

External Email - Use Caution Hello, I am working with a pediatric sample for which we are seeing many segmentation errors using the standard recon-all pipeline (version 7.3.2). Running synthseg on the same input files improves the segmentations dramatically, and I would like to be able to fix the surface files (?h.white, ?h.pial) according to the synthseg segmentation. I could not find how to do this in the documentation? Can I place the synthseg.nii.gz file somewhere and rerun recon-all? or autorecon? Would appreciate any pointers to the right way to go about this! Alternatively, I ran recon-all-clinical and that also seems to work well on our data, however the output folder is not identical to the standard recon-all folder, so I can not use that with other preprocessing pipelines that rely on freesurfer output (e.g. fmriprep). I would appreciate any advice on how to leverage the synthseg outputs instead of manually editing the segmentations! Thank you, Maya

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Freesurfer crash when loading "volume" surf
by Mirsol Choi 27 Oct '23

27 Oct '23

External Email - Use Caution Hi there, I have processed a t1 image using recon-all function, and when I try to open the surface file "lh.volume" or "rh.volume", freesurfer crashes everytime. This crash also occurs for other surface files as well, such as "lh.area.pial". Attached is the error message, do you know how I can go about this? For your reference I am using a macOS, running freesurfer 7.4.1. Thank you, I look forward to hearing from you. [image: Screen Shot 2023-10-26 at 6.41.05 PM.png] [image: Screen Shot 2023-10-26 at 6.41.55 PM.png]

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Re: [Freesurfer] Freesurfer crash when loading "volume" surf
by fsbuild 27 Oct '23

27 Oct '23

External Email - Use Caution If you have been launching Freeview using the Finder by double clicking on the icon, then try running it from the command line in a terminal to open a file, e.g. in bash or zsh ... $ export FREESURFER_HOME=/Applications/freesurfer/7.4.1$ source $FREESURFER_HOME/SetUpFreeSurfer.sh… output deleted ... … set the environment variable FS_LICENSE to point to your license file, e.g., put license.txt file you received via email after you registered into your home directory under /Users/<your userid> ... $ export FS_LICENSE=$HOME/license.txt$ head -1 $FS_LICENSEyou(a)somedomain.com.   <— email address you used to register with $ which freeview/Applications/7.4.1/bin/freeview … test displaying a known to be good volume … $ freeview  $SUBJECTS_DIR/bert/mri/brain.mgz If the above works, then try opening your file(s) from the command line instead of the volume file listed above. - R. On Oct 26, 2023, at 20:42, Mirsol Choi <mirsol(a)ualberta.ca> wrote:        External Email - Use Caution        Hi there, I have processed a t1 image using recon-all function, and when I try to open the surface file "lh.volume" or "rh.volume", freesurfer crashes everytime. This crash also occurs for other surface files as well, such as "lh.area.pial". Attached is the error message, do you know how I can go about this?For your reference I am using a macOS, running freesurfer 7.4.1.Thank you, I look forward to hearing from you. <Screen Shot 2023-10-26 at 6.41.05 PM.png><Screen Shot 2023-10-26 at 6.41.55 PM.png>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Linear Mixed Models for Functional Data
by Emily Iannazzi 26 Oct '23

26 Oct '23

External Email - Use Caution Hi there, We are trying to conduct functional linear mixed model analyses on our longitudinal (2 timepoint) data but are having trouble applying the structural documentation to functional data, particularly with the functions fs_read_label.m, fs_read.surf.m, and fs_read_Y.m. For instance, in the function [Y,mri] = fs_read_Y(‘lh.thickness.sm10.mgh’), which file should we be reading for functional data (instead of cortical thickness)? Additionally, do any of the subsequent steps (building design matrix, model specification, parameter estimation) require further information to be adapted for functional data? Any help would be greatly appreciated, Emily -- Emily Iannazzi (she/her) Adult Clinical Psychology University of Washington

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Stools error query
by Elizabeth Haris 25 Oct '23

25 Oct '23

External Email - Use Caution Hi there, I am running into a problem when using qatools.py to qa my recon-all. Some of my participants process ok, but with others I get the error below. Any advice on what to do to address this? Many thanks, Elizabeth ERROR: Computing white and gray matter SNR for orig.mgz ... Traceback (most recent call last): File "/Applications/freesurfer_v7.1.0/python/scripts/qatools.py", line 17, in <module> qatoolspython.run_qatools(subjects_dir, output_dir, subjects, shape, screenshots, fornix, outlier, outlier_table) File "/Applications/freesurfer_v7.1.0/python/packages/qatoolspython/qatoolspython.py", line 883, in run_qatools _do_qatools(subjects_dir, output_dir, subjects, shape, screenshots, fornix, outlier, outlier_table) File "/Applications/freesurfer_v7.1.0/python/packages/qatoolspython/qatoolspython.py", line 663, in _do_qatools wm_snr_orig, gm_snr_orig = checkSNR(subjects_dir, subject, SNR_AMOUT_EROSION, ref_image="orig.mgz") File "/Applications/freesurfer_v7.1.0/python/packages/qatoolspython/checkSNR.py", line 83, in checkSNR b_wm_data[x,y,z] = 1 IndexError: index 256 is out of bounds for axis 2 with size 256

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Re: [Freesurfer] Freeview issue
by fsbuild 22 Oct '23

22 Oct '23

External Email - Use Caution   The Qt graphics libraries may need virtualGl over a remote X connection.  So try prefacing your freeview command with "vglrun".  See the introductory text about vglrun and the install commands on this page, https://secure-web.cisco.com/1_jeLuB9K3YFX-_vkUZquNAqePEbWUSsW-inupVmdbjXle… Then once the remote display of images is working, you might run into an issue trying to map the display size to your remote screen resolution. - R. On 10/22/23 03:57, yunus soleymani (soleymani.yunus(a)yahoo.com) wrote:         External Email - Use Caution         I did the following codes respectively:> cd> wget MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/11GVLnIDWxo_vR8D2Oa9AP0rLkOmLrhl51L-g0K4pY8mWN… > ls freesurfer_ubuntu22-7.4.1_amd64.deb > sudo apt-get update -y > sudo apt-get -y install ./freesurfer_ubuntu22-7.4.1_amd64.deb > export FREESURFER_HOME=/usr/local/freesurfer/7.4.1 > echo "export FREESURFER_HOME=/usr/local/freesurfer/7.4.1" >> $HOME/.bashrc > ls $FREESURFER_HOME > ls license.txt > echo "export FS_LICENSE=$HOME/license.txt" >> $HOME/.bashrc > echo "export XDG_RUNTIME_DIR=$HOME/.xdg" >> $HOME/.bashrc > echo "export DISPLAY=:0" >> $HOME/.bashrc > echo "source $FREESURFER_HOME/SetUpFreeSurfer.sh" >> $HOME/.bashrc  ..................................................................................................................................................... The above codes all worked correctly and the software was installed successfully. Also, the software analyzes the subjects correctly by using parallel recon-all code. The only issue is that the Freeview interface doesn't work and the error mentioned above appears. Is it because of that I am using a remote desktop connection tool to connect to my institute servers? --------------------------------------------------------------------------------Yunus Soleymani Ph.D. Candidate of Neuroimaging Tehran University of Medical Sciences MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be soleymani.yunus(a)yahoo.com+98 914 526 9298-------------------------------------------------------------------------------- On Sunday, October 22, 2023 at 11:12:08 AM GMT+3:30, fsbuild <fsbuild(a)contbay.com> wrote:         External Email - Use Caution         Wondering if you used the freesurfer_ubuntu22-7.4.1_amd64.deb installer package from the download page and installed it from your Downloads folder via,$ sudo apt install ./freesurfer_ubuntu22-7.4.1_amd64.debThe link for that file on the downloads page MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1P6sJsKdfjhSOlm7uHbTXJ8nsEFCHNYGKzdj0djukhVoPC… R.On Oct 22, 2023, at 02:19, yunus soleymani <soleymani.yunus(a)yahoo.com> wrote:        External Email - Use Caution        I have the same problem. I would greatly appreciate your help with this.--------------------------------------------------------------------------------Yunus SoleymaniPh.D. Candidate of Neuroimaging Tehran University of Medical SciencesMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be soleymani.yunus(a)yahoo.com+98 914 526 9298--------------------------------------------------------------------------------On Saturday, October 21, 2023 at 12:24:10 PM GMT+3:30, Ramesh Babu <mgrameshbabu2013(a)gmail.com> wrote:        External Email - Use Caution        Dear Expert,Recently I installed the latest version of freesurfer in Ubuntu OS 22LTS.. Freesurfer is installed successfully, but freeview gives some errors which I pasted below. Please provide your suggestions. Thank YouRameshfreeview This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, webgl, xcb.Aborted (core dumped)_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1Z0_ffEGo83ss1m7kRMPeWTsWg7lKpmYawqoIi… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1gxLJVkQyQWy-mN2IV23c0x-Z-B3Llabbuqf9fFBFx5T4K… _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1CJwtL-NCVwbfYRfzulvtw0FqaswpVEEIEot84NQI4IAQZ… Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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Re: [Freesurfer] Freeview issue
by fsbuild 22 Oct '23

22 Oct '23

External Email - Use Caution  Wondering if you used the freesurfer_ubuntu22-7.4.1_amd64.deb installer package from the download page and installed it from your Downloads folder via, $ sudo apt install ./freesurfer_ubuntu22-7.4.1_amd64.deb The link for that file on the downloads page https://secure-web.cisco.com/1_35_maf1qeyDwN-YbnCQ8jOb6jvY5lINnAz… - R. On Oct 22, 2023, at 02:19, yunus soleymani <soleymani.yunus(a)yahoo.com> wrote:        External Email - Use Caution        I have the same problem. I would greatly appreciate your help with this.--------------------------------------------------------------------------------Yunus SoleymaniPh.D. Candidate of Neuroimaging Tehran University of Medical SciencesMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be soleymani.yunus(a)yahoo.com+98 914 526 9298--------------------------------------------------------------------------------On Saturday, October 21, 2023 at 12:24:10 PM GMT+3:30, Ramesh Babu <mgrameshbabu2013(a)gmail.com> wrote:        External Email - Use Caution        Dear Expert,Recently I installed the latest version of freesurfer in Ubuntu OS 22LTS.. Freesurfer is installed successfully, but freeview gives some errors which I pasted below. Please provide your suggestions. Thank YouRameshfreeview This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, webgl, xcb.Aborted (core dumped)_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1BZ4_HvToI5a6OuM5gIFWs2VyFinjkWLi8C5L5… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freeview issue
by Ramesh Babu 22 Oct '23

22 Oct '23

External Email - Use Caution Dear Expert, Recently I installed the latest version of freesurfer in Ubuntu OS 22LTS.. Freesurfer is installed successfully, but freeview gives some errors which I pasted below. Please provide your suggestions. Thank You Ramesh freeview This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, webgl, xcb. Aborted (core dumped)

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Re: [Freesurfer] fsxvfb error: Falling back to using screens root_visual
by fsbuild 20 Oct '23

20 Oct '23

External Email - Use Caution I could be wrong, but it reads like those errors are from the libqt5xcb.so running into errors communicating with X windows.   Since freeview runs fine displaying those images on the machine when not exec'd thru fsxvfb, then maybe fsxvfb cannot capture because it is not expecting freeview to (still) run using Qt graphics and X-windows .  I believe the release notes say fsxvfb does not need an X-server and so perhaps it is trying to capture images directly from the graphics hardware.  Could be something is not up to date on your system with the graphics hardware drivers/system libraries. Another thing to consider is the freesurfer 7.4.1 release was not built for nor tested on Ubuntu 16 - the minimum version tested was Ubuntu 18.   Given you are running it from the path /usr/global/freesurfer/7.4.1 then I suspect you did not download and run the 7.4.1 debian package installer for Ubuntu 18 as recommended on the freesurfer download page,  https://secure-web.cisco.com/1pa_Juw1rvYdwKxiYGrhHioNA_vUa-3QRuSL2A9WRhRTgv… (which would install under /usr/local/freesurfer).   It would not be surprising for the Ubuntu 18 binary installer to fail trying to update an Ubuntu 16 system, but you could try running it.  You can decline/abort the installation if you don't approve of the system updates it reports are needed before installing freesurfer.  Even if the installer succeeds, we can't guarantee 7.4.1 will work correctly on Ubuntu 16. - R. On 10/19/23 17:50, Dani Del Rubin (rubinstd(a)ohsu.edu) wrote: QXcbConnection: XCB error: 1 (BadRequest), sequence: 167, resource id: 133, major code:

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Freesurfer October 2023