Freesurfer

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30055 discussions

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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Postdoc Position - 7 Tesla MRI of Prefrontal Cortex - University of California, Berkeley
by Allison Chen 09 Jan '25

09 Jan '25

External Email - Use Caution Dear all, We seek a postdoctoral fellow to work on an NIH-funded project titled "Narrowing the mechanistic gap for anterior prefrontal cortex function" at the University of California Berkeley. This project targets the lateral aspect of anterior PFC, a brain region whose anatomy in humans is not clearly defined and whose fundamental role in cognition is poorly understood. At a descriptive level, aLPFC is involved in higher-level cognitive abilities such as planning, multi-tasking, reasoning, memory retrieval monitoring, and decision-making. Here, we seek to investigate its function at a more granular level in multiple ways, including high-resolution fMRI and diffusion-weighted imaging on the NexGen 7 Tesla scanner at the Brain Imaging Center at UC Berkeley. For any inquiries, please email Professor Bunge at sbunge(a)berkeley.edu For more information, please visit https://secure-web.cisco.com/1H2iagEP7blUXnY1sCQeJWL6MXuQYYM8L0YkLs3Uwl3BLE… Thanks, Allison

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SegmentAAN tool
by Todd L Richards 09 Jan '25

09 Jan '25

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 folder and 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 successfully but the SegmentAAN tool gives an error saying that it can't find SegmentNuclei from the run_segmentNuclei.sh: "${exe_dir}"/segmentNuclei $args command Please advise on how to fix this. Todd

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Any updates on thalamic nuclei mask in MNI space?
by Melissa Thalhammer 09 Jan '25

09 Jan '25

External Email - Use Caution Dear Freesurfer experts, is there a recent recommendation on how to get the thalamic nuclei segmentation into MNI space? I have tried the AAL3 atlas recommended in this previous mail (https://secure-web.cisco.com/1H8Dmv_kif-oWVc1HwepCKJBjRkpbig-MqiMJUrqPMzzu8…) but it contains only 15 instead of 26 nuclei per hemisphere. I have run recon-all and the ThalamicNuclei pipeline on the MNI-152 subject, which looks decent but wanted to make sure there is no better way? Thank you! Best, Melissa Thalhammer

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Error in recon-all
by Aaron Tanenbaum 09 Jan '25

09 Jan '25

External Email - Use Caution Hell All, I am testing recon-all and found that it returned with an error. I am not sure where the error is. The recon-all log file looks fine. I was testing a situation where we edit the wm.mgz and filled.mgz at the same time then run recon-all with -autorecon-wm. Attached is the recon-all log file. It should have all relevant info of version and description of our system. Any help would be appreciated. Thank you

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