Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30063 discussions

Re: [Freesurfer] recon-all errors (cannot execute binary file +
by fsbuild 16 Jan '24

16 Jan '24

External Email - Use Caution It looks like you did not use the .pkg file installer to install Freesurfer on the Mac, otherwise you would have a path like /Applications/freesurfer/7.4.1 to use as FREESURFER_HOME.  The installer should ensure the privileges should be correct to run commands.   There are several 7.X freesurfer releases, but the latest release is 7.4.1 and you can download it via the link, e.g., https://secure-web.cisco.com/1bTTDiznaFEJgJPDoi2yskrFqRdt_lNsr8LZ0PFjdBlc19… I would first remove what you have on your system from the terminal window with, $ sudo rm -rf /Applications/freesurfer Then in a Finder Window navigate to the Downloads folder (or to wherever you downloaded freesurfer-macOS-darwin_x86_64-7.4.1..pkg).  You should be able to RIGHT CLICK on that file, select open with the default pkg installer, and then enter your password etc. to install it.  Right clicking should bypass having to do some of the security exemptions in system preferences. Once the install is complete, setup the Freesurfer environment in the terminal window, $ export FREESURFER_HOME=/Applications/freesurfer/7.4.1$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /Applications/freesurfer/7.4.1 FSFAST_HOME       /Applications/freesurfer/7.4.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /Applications/freesurfer/7.4.1/subjects MNI_DIR           /Applications/freesurfer/7.4.1/mni You also need a license file, license.txt.  Once you complete the license request form at https://secure-web.cisco.com/1Svw39fuKLV2rL8mAOfpPDMZrLLodE_ScR0sKC… will receive a file “licesne..txt” via the email address used in the form.   Download/copy the license.txt file to your machine from the email. If your home directory is for example /Users/hyejung then you will see the following in the terminal window, $ cd$ pwd/Users/hyejung$ echo $HOME/Users/hyejung … if you downloaded license.txt into your Download folder ... $ cd Downloads$ ls license.txtlicense.txt$ cp -p -f  license.txt  $HOME/.$ cd $HOME$ ls license.txtlicense.txt You could also use the Finder to navigate and drag/drop the license.txt into your home directory.   Once it it there, set the environment variable FS_LICENSE so freesurfer commands will find the license when they run, $ export FS_LICENSE=$HOME/license.txt Then it should work to run freesurfer commands from the terminal window including freeview. - R. On Jan 16, 2024, at 20:47, 윤혜정 <hyejung7890(a)amc.seoul.kr> wrote:        External Email - Use Caution        Good day.When I run recon-all for my nii files I get either one of the following error messages:1. ERROR: could not configure recon-all parameters Killed 2. ERROR: could not configure recon-all parameters /Applications/freesurfer/bin/fspython: line 20: /Applications/freesurfer/python/bin/python3: cannot execute binary file /Applications/freesurfer/bin/fspython: line 20: /Applications/freesurfer/python/bin/python3: Undefined error: 0Or 3. a Pop Up message "_struct.cpython-38-darwin.so" cannot be opened because the developer cannot be verified. mac OS cannot verify that this app is free from malware. I googled the third error message and tried "Allow anyways" from the privacy setting. Then the next message pops up, then the next and the next. Could you please help me to understand the cause of the above 3 error messages? I tried to redownload freesurfer as well as python but none worked. Thank you in advance. Best,Alice_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Re: [Freesurfer] Freeview crashes when trying to load volumes
by fsbuild 16 Jan '24

16 Jan '24

External Email - Use Caution  It would help for us to know what your machine is running, e.g., linux or MacOS (Intel or Silicon Mac) - and what the version is for the operating system, e.g. Linux Ubuntu 22, MacOS 12, etc.  If you are running Linux on Windows thru either WSL or a VM then please mention that and if the Windows host is running Win 10 or 11. - R. On Jan 12, 2024, at 11:52, Ford, Jamie K <j.ford(a)imperial.ac.uk> wrote:        External Email - Use Caution        Hello,Please could I get some advice on my installation? I've downloaded version 7.4.0 using the same steps described in the installation video MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall?action=Attac… seems fine until I try to load any sort of volume, e.g., a Bert MRI file (like on the video). Freeview then crashes. This is the same for any volume. Could someone please advice? Any guidance would be greatly appreciated.Many Thanks,Jamie_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

Sample registration question
by Mirsol Choi 16 Jan '24

16 Jan '24

External Email - Use Caution Hi there Freesurfer, I am currently using freesurfer to take DTI metrics (FA, MD) from hippocampal subfields. At this point of my exploration with freesurfer, I am able to correctly register the hippocampal subfields and diffusion data, and obtain my FA values from the subfields. However, this is at the individual subject level. I will eventually need to register all of my samples in the same space for me to do a group analysis. However I am unsure what the order of registration should be for this process to be feasible. Does this order seem feasible for accurate analysis? 1) recon-all all of my subjects 2) dt_recon all of my subjects (one of the outputs is a registration file, which has registered the DTI data to outputs of recon-all) 3) run the hippocampus segmentation command on all subjects (segmentHA_T1.sh) to obtain hippocampal subfield segmentation 4) register the segmentation file to the FA maps (output of dt_recon) using vol2subfield command 5) After creating a subfield-FA map for each subject, spatial normalize the samples onto the same space using *mri_vol2vol* Thank you so much for taking the time reading my question. If there is a different method to spatially normalizing my datasets, or if there is a more optimal order of registration, I'd be happy to hear from you. Thank you, M

2 10

Midline white/pial surface
by Sunniva Fenn-Moltu 16 Jan '24

16 Jan '24

External Email - Use Caution Hi, i'm running recon-all and have encountered an issue with the surface boundaries on several subjects. What I'm experiencing is that the midline surface is included in the white surface in one hemisphere, and in the pial surface on the other hemisphere. This results in the midline boundary of the thalamus and ventral DC being white surface in one hemisphere, and pial surface in the other. Do you have any idea why this is happening? I am running freesurfer on NoMachine (freesurfer/7.4.1). Best, Sunniva

3 2

extracting measurements for mean gray matter thickness/LGI
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 16 Jan '24

16 Jan '24

External Email - Use Caution Hi, We were wondering what the preferred command is for extracting mean gray matter thickness/LGI I am aware that FS outputs left/right mean thickness but wanted to be conscious of the fact that left/right hemisphere might have different sizes. Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ---------------------------------------------------------------------- PLEASE NOTE: This message is intended for the use of the person to whom it is addressed. It may contain information that is privileged, confidential and exempt from disclosure under applicable law. If you are not the intended recipient, your use of this message for any purpose is strictly prohibited. If you have received this communication in error, please delete the message and notify the sender so that we may correct our records. See our web page at http://secure-web.cisco.com/1BNvfJRjX0fEnr3nm7iMFhLObCbrotFPlWBRQsG1XTL9Ssf… for a full directory of Beth Israel Lahey Health sites, staff, services and career opportunities.

2 3

fsLR label to fsnative annotation
by Bram Diamond 16 Jan '24

16 Jan '24

External Email - Use Caution Dear FreeSurfer experts, Happy new year! I hope you all are doing well! I recently wrote the following question to the HCP-User Google Group and was directed to cross-post in the FreeSurfer list server by Dr. Matt Glasser. I have created individualized rs-fMRI maps as dlabel fsLR 32k space using Kong et al. (2021)<https://secure-web.cisco.com/1YPDKOJqHMz1SpGXNYNBBQj7WFDd_y7LiRNZ1juccRfmSk…> and I would like to resample them to a FreeSurfer annotation in anatomical space without losing individual parcel assignments. The method below resamples the maps but loses parcel assignments. echo "running -cifti-seperate" wb_command \ -cifti-separate \ $dlabel_in \ COLUMN \ -label CORTEX_LEFT $dlabel_dir/${dlabel_in_base_name}.L.fsLR_32k.label.gii \ -label CORTEX_RIGHT $dlabel_dir/${dlabel_in_base_name}.R.fsLR_32k.label.gii for hemi in L R; do gii_in=$dlabel_dir/${dlabel_in_base_name}.${hemi}.fsLR_32k.label.gii sphere_in=$standard_dir/resample_fsaverage/fs_LR-deformed_to-fsaverage.${hemi}.sphere.32k_fs_LR.surf.gii sphere_out=$standard_dir/resample_fsaverage/fsaverage_std_sphere.${hemi}.164k_fsavg_${hemi}.surf.gii gii_out=$dlabel_dir/${dlabel_in_base_name}.${hemi}.fsaverage_164k.label.gii area_in=$standard_dir/resample_fsaverage/fs_LR.${hemi}.midthickness_va_avg.32k_fs_LR.shape.gii area_out=$standard_dir/resample_fsaverage/fsaverage.${hemi}.midthickness_va_avg.164k_fsavg_${hemi}.shape.gii echo "running -label-resample for "$hemi"" wb_command \ -label-resample \ $gii_in \ $sphere_in $sphere_out \ ADAP_BARY_AREA \ $gii_out \ -area-metrics \ $area_in $area_out hemilower=$(echo $hemi | tr '[:upper:]' '[:lower:]') fshemi=${hemilower}h annot_out=${out_dir}/${fshemi}.${dlabel_in_base_name}.fsaverage.annot echo "running mri_convert for "$fshemi"" mris_convert \ --annot $gii_out \ $FREESURFER_HOME/subjects/fsaverage/surf/${fshemi}.pial \ $annot_out echo "running mri_surf2surf" mri_surf2surf \ --srcsubject fsaverage \ --trgsubject $sub_id \ --hemi $fshemi \ --sval-annot $annot_out \ --tval $SUBJECTS_DIR/$sub_id/label/${fshemi}.${dlabel_in_base_name}.${sub_id}.annot \ --sd ${SUBJECTS_DIR} mri_segstats \ --annot $sub_id $fshemi Ind_parcellation_MSHBM_${sub_num}_w20_MRF5.${sub_id} \ --i $SUBJECTS_DIR/$sub_id/surf/${fshemi}.thickness \ --sum ${out_dir}/${fshemi}.Ind_parcellation_MSHBM_${sub_num}_w20_MRF5.${sub_id}.thickness done The original dlabel has a parcel label table with the following column names, "KEY" (int, 0-400), "NAME" (string, detailed below), and "RED, "GREEN," "BLUE," "ALPHA" for RGB/1 (image_1). NAME is <atlas_hemi_network_region_int>, where atlas is always "17networks," hemi is "LH" or "RH," network is one of 17 networks (e.g., "DefaultA"), region is ≥1 unique anatomical region for each network (e.g., "FPole" and "IPL" for "DafaultA"), and int is an integer ID for repeat parcels in the same network and region (e.g., "DefaultA_IPL_1" and "DefaultA_IPL_2"). However, when converted to a FreeSurfer annotation file using the method above, parcels are collapsed across <network> and the name is taken from the first instance (image_2). For example, I have parcels "17networks_LH_DefaultA_IPL_1" and "17networks_LH_DefaultA_IPL_2" in the dlabel, but only a single label called "17networks_LH_DefaultA_IPL_1" including the two parcels in the annotation file. This is also occurring across hemispheres, where "17networks_RH_DefaultA_IPL_1" and "17networks_RH_DefaultA_IPL_2" (both on the right hemisphere) are both included in a single "17networks_LH_DefaultA_IPL_1" label in the rh.parcellation.annot file. Notably, the networks assignment appears correct in FreeSurfer native space. However, I would like the networks to remain parcellated for morphometric analyses. Any help would be greatly appreciated. Bram Bram R. Diamond, MS Clinical Psychology Doctoral Candidate Northwestern University Feinberg School of Medicine Mesulam Center for Cognitive Neurology & Alzheimer’s Disease 300 E. Superior Street | Tarry 8 | Chicago, IL 60611 http://secure-web.cisco.com/1hcjqpWwkL0-_XOMzF0mEIJ3Zgf7lJaA2354VSSviOf-Fxm…<http://secure-web.cisco.com/1hcjqpWwkL0-_XOMzF0mEIJ3Zgf7lJaA2354VSSviOf-Fxm…>

2 1

Postdoc position in Medical Image Computing
by Diers, Kersten /DZNE 15 Jan '24

15 Jan '24

External Email - Use Caution The German Center for Neurodegenerative Diseases (DZNE) is a world- leading internationally oriented research center, committed to discovering new approaches to prevent and treat neurodegenerative diseases. To this end, researchers at ten DZNE sites across Germany pursue a translational and interdisciplinary strategy comprising five interconnected areas: fundamental research, clinical research, health care research, population health science, and systems medicine. We are looking for a postdoctoral researcher in Medical Image Computing to join the research group of Prof. Martin Reuter (DeepMI Lab) at the German Center for Neurodegenerative Diseases (DZNE) in Bonn, Germany. The research focus of the DeepMI lab (https://secure-web.cisco.com/1MThzC1peUCNro2lFQjLKa18yzb6Hpg-Si0c_KIJ2lS10s…) is on the development of novel AI methods for the automated analysis of medical images, and on providing accessible and useful open-source software tools for the medical imaging community. In addition to medical image computing and computational neuroimaging, our research interests include computational geometry and topology, computer vision, and statistical modeling. In close collaboration with clinical and industrial partners, we develop the next-generation computational techniques and open-source software tools (https://secure-web.cisco.com/1x5I_D6HZMoyenb6ROM07HEyfo1-6i4RLvoIUTkcQNenQo…) for the analysis of large biomedical image datasets – such as FastSurfer (https://secure-web.cisco.com/18DvIli8JaO37YJWJOJ3qq1WWQmz42f76xdZHIj0fW_8UF…) a fast and extensively validated deep-learning pipeline for the automated processing of structural human brain MRIs that is used by neuroimaging researchers worldwide. Our network within DZNE and the University Clinic Bonn, as well as our close ties to the Harvard Medical School promote our interdisciplinary research and foster deep international collaborations. Creative, highly motivated applicants who are willing to develop novel deep learning image analysis methods and enjoy teamwork and working independently in a stimulating scientific environment are encouraged to apply. Requirements: - PhD degree in Computer Science or a related discipline; candidates who are expected to complete their PhD degree soon will also be considered. - Solid background in Machine Learning / Deep Learning and strong computational skills. - Programming experience (Python) and familiarity with Machine Learning Frameworks (e.g., PyTorch, Tensorflow). - Experience in magnetic resonance imaging, medical image analysis, and/or computer vision is an advantage. To apply, please upload your application including a cover letter stating your motivation and research interests, CV, relevant transcripts and up to two references via the following link: https://secure-web.cisco.com/1T2gF-0AOy7jeB4jbnIw5lbkhOm3NWFidBlXUXn7AZpaMD… The application deadline is January 30, 2024. Review of applications will begin immediately and continue until the position is filled.

1 0

Parallel Command for Windows
by ERNEST KISSI 13 Jan '24

13 Jan '24

External Email - Use Caution Hi Freesurfer team, Please can I run the parallel Command for freesurfer? I am using windows 11.

1 0

Registration of MPF to FLASH 3D image
by ERNEST KISSI 12 Jan '24

12 Jan '24

External Email - Use Caution Dear Freesurfer team, I messaged the team on my MPF map analysis and a suggestion was made that I register the MPF maps on the T1 MPRAGE images. However, I did not acquire MPRAGE but FLASH images. Can I used those instead ? Again, I tried even using only the T1 FLASH images and it did not work so I am not sure whether the registration of the MPF maps on it will work or not. Is there anyway around this? Thank you.

3 5

Re: [Freesurfer] Trouble with ssh tunneling & Freeview
by fsbuild 12 Jan '24

12 Jan '24

External Email - Use Caution A remote connection working to display images from the glxgears or xeyes commands run on the linux host forwarded to your local machine does not mean Freeview graphics will do the same.  If Freeview still displays an empty or black screen, then there could be issues with OpenGL graphics running on or being sent from the linux host.   The system requirements for Freesurfer include the following for running Freeview, Graphics card: 3D graphics card with its own graphics memory & accelerated OpenGL drivers Updating the OpenGL drivers on the linux host will sometimes enable Freeview to display images remotely.  My understanding is Linux servers need Mesa packages installed to support newer versions of OpenGL.  If the Freesurfer Debian or RPM package installer was used to install the Freesurfer distribution on the Linux host, then at least some of those packages should now be installed, i.e., we do not recommend using the tar archive to “install” Freesurfer.  We don’t know how EXPANSE installs/maintains Freesurfer or what their servers support for graphics hardware. GLX is the X-windows extension for OpenGL graphics that can be tunneled thru a remote SSH connection.  But GLX may not work with the newer versions of OpenGL over ssh.  A workaround for this is to install and use VirtualGL on the Linux host.  If VirtualGL is supported/installed on EXPANSE, try prefacing the freeview command with “vglrun” - see https://secure-web.cisco.com/10kzDiIcCSK5wSi3KZ4WHry8djBXAuam589oK…  We use VirtualGL and graphics acceleration on a few Linux workstations to accommodate Freeview running on Linux and viewing its 3D graphics thru a remote VPN connection. XQuartz on the Mac is the equivalent of X-Windows on Linux.   The Mac should be using Xquartz 2.8.2 or newer for use with the Freesurtfer 7.4.X releases.  I think X-Quartz will open automatically to view X-Windows based graphics on the Mac. If the EXPANSE linux machines are setup to support remote connections to view 3D X-windows graphics then the IT support staff will know about the options above.  File/open a ticket with them, ask them what they support, and how to setup your environment.  If they do not support it, an alternative is to install Freesurfer on your Mac and download/copy over the data to view with Freeview. - R. On Jan 11, 2024, at 14:18, Dong, Yilei <yid025(a)health.ucsd.edu> wrote:        External Email - Use Caution        Hi Freesurfer team, I have Freesurfer installed on UCSD's Expanse HPC, which uses the Rocky Linux 8 operating system. Whenever we try to do ssh tunneling and more specifically, logging into our HPC via ssh -X to open up Freeview's GUI, it always aborts. Prior to logging into my HPC from my Mac laptop's terminal, I always open up XQuartz. Another colleague of mine has also encountered similar issues, where they have managed to get X11 and Xeyes to run, but also Freeview's window keeps aborting. We have also tried to follow instructions from the following links when it comes to getting ssh tunneling to work correctly in hopes of making Freeview's GUI pop up: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://http://secure-web.cisco.com/12UaY28IjOvcCuzqwhVkemgeWWYzbyjV_gOl5… has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/13jhlKniK4ot1jAvrTEdLmUxfeVBEFlM0Xf3YM… we operate from a Mac computer, is it better to use a VNC or XQuartz for ssh tunneling? In addition, can we find an error log in Freesurfer's directory to find out exactly why Freeview keeps aborting in our circumstance?Thank you. Sincerely,Yilei <Screen Shot 2024-01-11 at 11.01.27 AM.png>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer