Freesurfer

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12 participants
30060 discussions

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

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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.

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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…>

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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.

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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.

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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.

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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

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Including superficial white matter in cortical parcellation
by Thomas, George 12 Jan '24

12 Jan '24

External Email - Use Caution Dear Freesurfer Experts, I am interested in generating a volumetric segmentation and parcellation of the HCP-MMP1 atlas using mri_surf2volseg - and I have previously done this like so: mri_surf2volseg --o $sub/HCP-MMP1_fsSpace.mgz \ --label-cortex --i $sub/mri/aseg.mgz --threads 4 \ --lh-annot $sub/label/lh.HCP-MMP1.annot 1000 --lh-cortex-mask $sub/label/lh.cortex.label \ --lh-white $sub/surf/lh.white --lh-pial $sub/surf/lh.pial \ --rh-annot $sub/label/rh.HCP-MMP1.annot 2000 --rh-cortex-mask $sub/label/rh.cortex.label \ --rh-white $sub/surf/rh.white --rh-pial $sub/surf/rh.pial However rather than use the regular white matter surface generated by recon-all (as above), I want to parcellate between the pial surface and a superficial white matter surface 1mm below the GM/WM boundary. I have generated this superficial white matter (SWM) surface for both hemispheres like so: mris_expand lh.white -1 lh.SWM.1mm My first though was just to replace the --rh-white / --lh-white inputs with the SWM surface, but after running this, the output remains the same. I think I may also need use a different input than aseg.mgz, but not sure what this would be or how to generate it. Any assistance you could offer with the would be greatly appreciated. Many thanks, George

2 1

poor inferior cerebellum segmentation
by Carlos Alcocer 12 Jan '24

12 Jan '24

External Email - Use Caution Hello, Inferior portion of cerebellum are not segmented well. It is included in skullstrip and I tried adding control points in cerebellar WM but this did not help. I am not interested in cerebellum but I do need eTIV. Will this poor cerebellar segmentation affect eTIV calculation? Thank you, Carlos

4 3

Issue with mri_glmfit-sim
by O'Neill, Alexandra Grace 12 Jan '24

12 Jan '24

Hello FS community, To correct for multiple comparisons for the results of a parametric modulation GLM analysis, I have run mri_glmfit-sim using Freesurfer version 6.0 with the following command: mri_glmfit-sim \ --debug --glmdir /cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepSec/OSGM/osgm \ --perm 1000 2.0 abs \ --cwp 0.05 \ --2spaces \ --bg 1 The code completes without errors, however none of the output files mentioned in this tutorial<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.…> are created. Below are the contents of the mriglm-fit.log file in case that is helpful. $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd /autofs/cluster/eryilmaz/users/NFE/NFE_Subjects_ago cmdline mri_glmfit.bin --y /cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/ces.nii.gz --wls /cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/cesvar.nii.gz --fsgd /cluster/eryilmaz/users/FSGD/18_NFE_Patients.fsgd --osgm --glmdir /cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/OSGM --surf fsaverage rh --fwhm 6 sysname Linux hostname tempest.nmr.mgh.harvard.edu machine x86_64 user ago5 FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 fwhm 6.000000 niters 26.000000 OneSampleGroupMean 1 y /autofs/cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/ces.nii.gz logyflag 0 usedti 0 FSGD /cluster/eryilmaz/users/FSGD/18_NFE_Patients.fsgd labelmask /cluster/eryilmaz/users/NFE/NFE_Subjects_ago/fsaverage/label/rh.cortex.label maskinv 0 glmdir /cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/OSGM IllCondOK 0 ReScaleX 1 DoFFx 0 wFile /cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/cesvar.nii.gz weightinv 1 weightsqrt 1 ResidualFWHM 12.847434 SearchSpace 74490.844410 anattype surface Do you have any idea how to fix this problem? Thanks so much in advance! Alexandra Alexandra G. O'Neill (she/her) Clinical Research Coordinator Massachusetts General Hospital Department of Psychiatry Division of Neuropsychiatry and Neuromodulation 149 13th Street, Charlestown, MA 02129 T: (617) 726-8753 | E: agoneill(a)mgh.harvard.edu<mailto:agoneill@mgh.harvard.edu>

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