Freesurfer January 2025

freesurfer@nmr.mgh.harvard.edu

44 participants
67 discussions

Re: [Freesurfer] NextBrain: no segment_fast or segment_fireants.py
by fsbuild 20 Jan '25

20 Jan '25

External Email - Use Caution   FS_HOME/python/packages/ERC_bayesian_segmentation/scripts/segment_fast.py isn’t in the 7.4.1 release from June of 2023 (now 2 years old).  You would need to switch to an install of one of the more recent packages from one of the development builds which you can find under, https://secure-web.cisco.com/1C2Ar2D42F31zW_7LdVanyLS5o5uQzqY0lbs-9lUFxdV56… There are some caveats that go along with switching to a different release, Important Note: When processing a group of subjects for your study, it is essential to process all your subjects with the same version of FreeSurfer, on the same OS platform and vendor, and for safety, even the same version of the OS. While we continue to work to ensure that results match across platforms, there are none-the-less system-level libraries that are OS dependent. An exception to this rule is that you may view and edit files across any platform or version, and run some post-processing tools (outside the recon-all stream) if you check with us first (for instance you may run the longitudinal processing with newer versions). - R. On Jan 20, 2025, at 05:54, AmirHussein Abdolalizadeh <amirhussein.a(a)gmail.com> wrote:        External Email - Use Caution        Hi Freesurfer users/experts, I was trying to run NextBrain (cloned from here: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/14eLrRV3Lqib6Tav7bYz9kPh7vG-KbczSql2Ct…) and asked HPC admin to install atlas_full and atlas_simplified in the designated folders, but encountered this error that segment_fast.py is not available in FS_HOME/python/packages/ERC_bayesian_segmentation/scripts/segment_fast..py (or segment_fireants.py). The code I run (in the folder of the downloaded tool):./mri_histo_atlas_segment_fireants /path/to/input/T1.nii.gz /path/to/output/folder 0 dct I'm using FreeSurfer 7.4.1. Any help would be appreciated. Best,Amir _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1CDVwd9EaNYDWvqQc8hMimAN9CIoe95--mDhbMVqe2jheP…

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Re: [Freesurfer] Freesurfer remotely processing
by fsbuild 20 Jan '25

20 Jan '25

External Email - Use Caution  The freesurfer mri* commands can be run from a terminal window remotely via ssh’ing into a machine that has access to a local installation of freesurfer.  Hopefully your network connection is robust enough to keep up with your typing in the terminal shell window, and can display continuous output from the freesurfer commands you run. An X-windows server needs to be available on the machine where freeview runs in order to display the brain graphic images.   If you are going to run freeview on a remote machine, then X-Windows forwarding along with (hopefully some accelerated) Open GL graphics rendering is often setup so the images can be rendered there and then forwarded over the network to your machine.  That is faster/more efficient then trying to push more of the graphics over the network to be rendered with your local machines graphics hardware.  NoMachine, TightVNC, etc. could help with creating that connection. If you have an IT department, you should check with them to see if they already have specific machines setup for you to remotely login to - including forwarding images from X-Windows apps (like freeview) over the network to your machine. - R. On Jan 20, 2025, at 09:57, Fischl, Bruce R.,PHD <BFISCHL(a)mgh.harvard.edu> wrote:Hi Gonzalo Can you clarify what you mean? People use ssh all the time to log into remote machines and run recon-all (and freeview) CheersBruce From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of Gonzalo Rojas Costa Sent: Monday, January 20, 2025 7:12 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Freesurfer remotely processing         External Email - Use Caution        Hi:Is there any free implementation that allows me to process images with freesurfer remotely?Sincerely Gonzalo Rojas CostaMedicine SchoolFinis Terrae University_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer remotely processing
by Gonzalo Rojas Costa 20 Jan '25

20 Jan '25

External Email - Use Caution Hi: Is there any free implementation that allows me to process images with freesurfer remotely? Sincerely Gonzalo Rojas Costa Medicine School Finis Terrae University

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consensus on mp2rage or other t1w mri at 7T
by Jiaen Liu 17 Jan '25

17 Jan '25

External Email - Use Caution Dear community I'm wondering if there is a good consensus paper or other resources that can summarize the best practices of using high resolution T1w MRI at 7T and Freesurfer? We have a lot of mp2rage data which has nice uniformity but is affected by the background/skull noise. We use the second inversion time image INV2 to extract a brain mask to mitigate the issue. I'm not sure that's the best way. There are also tools like the robust mp2rage combination or the mprageise to remove the noise. We haven't systematically tested them yet. I'm wondering if these have been done and we can learn from previous experience. Thanks! Best regards, Jiaen Liu Ph.D. Assistant Professor Advanced Imaging Research Center & Radiology UT Southwestern Medical Center 2201 Inwood Ln Dallas, TX, USA, 75390 Office: 214.645.2750 Website: Liu (Jiaen) Lab | UT Southwestern, Dallas, Texas<https://secure-web.cisco.com/1k3jFgucLlYfBOkzupHE_iJP9vYs_l28g57vFBZ0AYA2d3…> ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Issue with mri_histo_atlas_segment_fireants Command
by Taghizadeh Mortezaei, Nima 13 Jan '25

13 Jan '25

Dear FreeSurfer Developers and Community, I am trying to run Bayesian Segmentation with the Histological Atlas "NextBrain" in FreeSurfer. I have already downloaded and uncompressed the atlas into the ERC_bayesian_segmentation folder. However, when I attempt to proceed, I encounter the following error: zsh: command not found: mri_histo_atlas_segment_fireants I am using FreeSurfer version freesurfer-macOS-darwin_x86_64-8.0.0-beta-20241103-b8aacdc. Could you please let me know if this command is supported in my version or if I am missing any setup steps? Thank you for your assistance. Best regards, Nima Taghizadeh Mortezaei, M.D. Radiation Oncology Research Fellow, MGH

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Missing Choroid Plexus Segmentation in final output
by Taghizadeh Mortezaei, Nima 13 Jan '25

13 Jan '25

Dear FreeSurfer Developers and Community, I recently ran recon-all-clinical using FreeSurfer version freesurfer-macOS-darwin_x86_64-8.0.0-beta-20241103-b8aacdc on a T1-weighted axial post-contrast MRI. However, I noticed that the choroid plexus is neither segmented nor labeled in the aseg.mgz or synthseg.mgz files in the final output. I would greatly appreciate it if anyone could help me understand or resolve this issue. I have attached the log file for reference. Thank you for your assistance. Best regards, Nima Taghizadeh Mortezaei, M.D. Radiation Oncology Research Fellow, MGH

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New user
by allio34218＠aol.com 13 Jan '25

13 Jan '25

External Email - Use Caution Hi, I was wondering if anyone can point me to a good tutorial that would focus on how to upload and process DICOM data into FS / FreeView. I have a recent Triage Brain Atrophy report from NeuroQuant and would like to see how this compares to results generated in FS. I am a brand-new user and just installed FS on my computer. Thank you,Allison O.

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Re: [Freesurfer] freeview slow in vnc
by fsbuild 13 Jan '25

13 Jan '25

External Email - Use Caution  Do the other remote apps you report are working fine also display 2D/3D graphics as freeview does, e.g., with a surface or volume loaded?    If not, your comparison may not be valid as the remote server running freeview could be doing more work trying to push graphics over the network to display on your machine compared to the other apps.   TigerVNC can be sluggish or slow down for remote X-Windows applications (like freeview) if they are running on a server not setup to use accelerated X-WIndows graphics for remote connections.   That usually depends upon how your IT department has setup your remote servers and maybe configured how TigerVNC connects from your machine. - R. On Jan 12, 2025, at 16:13, Jiaen Liu <Jiaen.Liu(a)utsouthwestern.edu> wrote:        External Email - Use Caution        I use freeview through a vnc session and the client tigervnc. It happened that freeview suddenly becomes very slow even without loading any data. The GUI becomes slow in responding to clicking the menu items. Other apps in the same session are normal. Does anyone have this experience?Thanks! Best regards,Jiaen Liu Ph.D.Assistant ProfessorAdvanced Imaging Research Center & RadiologyUT Southwestern Medical Center2201 Inwood LnDallas, TX, USA, 75390Office: 214.645.2750Website: Liu (Jiaen) Lab | UT Southwestern, Dallas, Texas UT SouthwesternMedical CenterThe future of medicine, today._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] SegmentAAN tool
by fsbuild 13 Jan '25

13 Jan '25

External Email - Use Caution There was an issue with SegmentAAN for some OS's at the time of the beta build, so I suggest you download and do a real install of the current Ubuntu 22 dev build by downloading the package, https://secure-web.cisco.com/1jtCE3QdoKwQOY25B7jTfo4lrPoTLOS3… … then cd to the download location and install with the apt commands, $ sudo apt remove freesurfer$ sudo apt install ./freesurfer_ubuntu22-7-dev_amd64.deb That should install such that FREESURFER_HOME and the setup off the environment should now be, $ export FREESURFER_HOME=/usr/local/freesurfer/7-dev$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-linux-ubuntu22_x86_64-dev-20250112-a90fba7 --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /usr/local/freesurfer/7-devFSFAST_HOME       /usr/local/freesurfer/7-dev/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /usr/local/freesurfer/7-dev/subjectsINFO: /home/rd521/matlab/startup.m does not exist ... creatingMNI_DIR           /usr/local/freesurfer/7-dev/mni $ which run_segmentNuclei.sh /usr/local/freesurfer/7-dev/bin/run_segmentNuclei.sh $ which segmentNuclei/usr/local/freesurfer/7-dev/bin/segmentNuclei Don’t forget to set your SUBJECTS_DIR to some path not under the protected system install path /usr/local which requires sudo permission to write to.  So for example you could set SUBJECTS_DIR to be somewhere you always have non-sudo write permission like your home directory, e.g., $ export SUBJECTS_DIR=$HOME/my_subjects We discourage using the tar archive and recommend running the actual installer package since the tar archive does not check for or install dependencies the freesurfer binaries may need to run on the system. - R.On Jan 9, 2025, at 09:33, Todd L Richards <toddr(a)uw.edu> wrote:        External Email - Use Caution        I have installed  the following version of freesurfer on my ubuntu computer freesurfer-linux-ubuntu22_x86_64-8.0.0-beta.tar.gz and I have linked ln -s to my installation of matlab folderand I am trying to use the tool called SegmentAAN which does exist on this version of the and tried to execute this tool for a subject that already has had recon-all -all -s sub-01 run on it successfullybut the SegmentAAN tool gives an error saying that it can't findSegmentNuclei from therun_segmentNuclei.sh:  "${exe_dir}"/segmentNuclei $args command Please advise on how to fix this.Todd _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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freeview slow in vnc
by Jiaen Liu 12 Jan '25

12 Jan '25

External Email - Use Caution I use freeview through a vnc session and the client tigervnc. It happened that freeview suddenly becomes very slow even without loading any data. The GUI becomes slow in responding to clicking the menu items. Other apps in the same session are normal. Does anyone have this experience? Thanks! Best regards, Jiaen Liu Ph.D. Assistant Professor Advanced Imaging Research Center & Radiology UT Southwestern Medical Center 2201 Inwood Ln Dallas, TX, USA, 75390 Office: 214.645.2750 Website: Liu (Jiaen) Lab | UT Southwestern, Dallas, Texas<https://secure-web.cisco.com/1LClKYkRkBpNH_pS8UME-BWJLG-ZeHMTLBQ5-g4msEr3Nm…> ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Freesurfer January 2025