Freesurfer

freesurfer@nmr.mgh.harvard.edu

5 participants
30053 discussions

Normalization of cervical cord area or volume
by AJ 03 Feb '26

03 Feb '26

External Email - Use Caution What’s the best way of normalizing spinal cord area or volume: by TIV, brain volume, or regression? All these methods are used, but wanted your expert opinion Many thanks. AJ

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recon-any on the dev version: MODEL NOT FOUND
by Hajer Karoui 03 Feb '26

03 Feb '26

External Email - Use Caution Hello, I am trying to build my recon-any docker container, however, there aren't any recon-any models under /usr/local/freesurfer/models . I used the dev version as instructed on the recon-any page<https://secure-web.cisco.com/1IWMAnbFsrK7hUPXbUYFFyownliON0lfj8kai-AYb1tFVM…> : https://secure-web.cisco.com/1wqyV9QaH0DR_i5QozZC-H1CIPo692K7W9DuzDSMFhjOld… The line in the recon-any script (on the github repo<https://secure-web.cisco.com/1Y6OZwVR9AsipMHQdhwC2Wt__u5i2tFQbtRNBzaKMK2KTM…>) to download the model contains a work that doesn't actually work. I get Exit code 8 from wget (server error / HTTP error). So the URL is likely wrong or the file doesn't exist at that location. https://secure-web.cisco.com/1qWCICkPxU-ruG3rUhQv-XwI8SbaLM4OiAg-DKIR3Xbp1P… Looking forward to your advice and thanks. Best regards, Hajer Karoui Research Assistant | PhD Student King's College London Centre for Neuroimaging Sciences LinkedIn<https://secure-web.cisco.com/1m-CuDAw710ERnIYdy9wPywd9tq2n2rHaqU9MWNw-h0t4X…> [cid:d18f3379-74d7-4db2-8404-74031e6a6706] UNITY<https://secure-web.cisco.com/1MANCssXgEvlewAf2IUiy48lbi4V8lg_RU7S56W3fR0TAe…>

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Issue accessing WMH-Synthseg required files
by Cui, Qiming 02 Feb '26

02 Feb '26

External Email - Use Caution Dear Freesurfer team, I am trying to use mri_WMHSynthseg for white matter hyperintensity segmentation. I have installed the latest dev version, and I understand I need to download an atlas file from " https://secure-web.cisco.com/1rKqiV3c2UqdiIsJcAkgN6Rp80ECVnAQhuP-ybfrZvES9u…". However, I get a 404 error when I try to access this url. Upon examining the server, I see that https://secure-web.cisco.com/1mPu-NE2sUuQ7fyqENpvjVu3_TN_mht4HgGfcxc1kLZmIQ… is empty. Could you help me gain access to this atlas file? Thank you. Best, Gavin Cui

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Electrode coordinate transformation to MNI152 space
by Kerezoudis, Panos, M.D., M.S. 01 Feb '26

01 Feb '26

External Email - Use Caution Hi, I have run the cvs registration to MNI152 space on my subject’s T1 nifti volume (‘cvs_avg35_inMNI152’). Process was uneventful and the necessary files were generated. How do I convert now the intracranial electrode coordinates from native to MN152 space? I have stored the coordinates in a .txt file, essentially as a matrix, channels by xyz physical coordinates (AC=center of origin). I have not been able to find anything helpful online. Thank you very much in advance, Panos Kerezoudis

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(无主题)
by 13699676540 01 Feb '26

01 Feb '26

External Email - Use Caution help

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我想要安装我需要安装
by 13699676540 01 Feb '26

01 Feb '26

External Email - Use Caution 我需要安装包

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Regarding Collaboration and Partnerships
by Ozgur Akbulut 31 Jan '26

31 Jan '26

External Email - Use Caution Dear Sir or Madam, We are a company established in Turkey under the names beyinverimerkezi.com and braindatacenter.com, dedicated to providing measurement and reporting of brain volumetric values to MR Imaging Centers, private hospitals, and the Turkish Ministry of Health. Our primary objective is to deliver the data we obtain to neurologists, psychiatrists, and neurosurgeons prior to diagnosis, thereby guiding early detection and treatment strategies, as well as evaluating the efficacy of implemented treatments through controlled measurements. In pursuit of this goal, we would like to request an online meeting to explore opportunities for collaboration, integration to your ecosystem, and assuming roles that will contribute to the development processes. The meeting will include participation from our Turkish team: Prof. Dr. Niyazi Acer, who received his training at Johns Hopkins University; our software partner, Özgür Akbulut; and Turgay Şahin, the brain researcher and originator of the core concept. We eagerly anticipate discussing a suitable date and time, taking into account the time difference between our locations. We extend our profound gratitude to every FreeSurfer volunteer for their invaluable contributions to the field. Özgür Akbulut CTO - Brain Data Center ozgurakbulut(a)braindatacenter.com http://secure-web.cisco.com/1Nv6cgLfVYARoj7aVwFaISaxYAGpnS9POwcvMOuJue_MIHT… +90 533 541 19 00

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Regarding Collaboration and Partnerships
by info＠braindatacenter.com 31 Jan '26

31 Jan '26

External Email - Use Caution Dear Sir or Madam, We are a company established in Turkey under the names beyinverimerkezi.com and braindatacenter.com, dedicated to providing measurement and reporting of brain volumetric values to MR Imaging Centers, private hospitals, and the Turkish Ministry of Health. Our primary objective is to deliver the data we obtain to neurologists, psychiatrists, and neurosurgeons prior to diagnosis, thereby guiding early detection and treatment strategies, as well as evaluating the efficacy of implemented treatments through controlled measurements. In pursuit of this goal, we would like to request an online meeting to explore opportunities for collaboration, integration to your ecosystem, and assuming roles that will contribute to the development processes. The meeting will include participation from our Turkish team: Prof. Dr. Niyazi Acer, who received his training at Johns Hopkins University; our software partner, Özgür Akbulut; and Turgay Şahin, the brain researcher and originator of the core concept. We eagerly anticipate discussing a suitable date and time, taking into account the time difference between our locations. We extend our profound gratitude to every FreeSurfer volunteer for their invaluable contributions to the field. Özgür Akbulut CTO - Brain Data Center ozgurakbulut(a)braindatacenter.com http://secure-web.cisco.com/1ADYhfrm1D5yD7eBi9ik3wPlCDLf0aUJ937KGbH28CBHRzW… [1] +90 533 541 19 00 Links: ------ [1] http://secure-web.cisco.com/1ADYhfrm1D5yD7eBi9ik3wPlCDLf0aUJ937KGbH28CBHRzW…

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Fwd: recon-all doesn't find 001.mgz in mri/orig
by Angelika Wolman 30 Jan '26

30 Jan '26

External Email - Use Caution Hello FreeSurfer Developers,I'm attempting to compute recon-all on my nii files. It seems it doesn't find 001.mgz in mri/orig *Subject does not have a bstampfile, copying /opt/fox_cloud/share/app/imaging/freesurfer/7.3.2-1/build-stamp.txt* I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.3.2-20220804-6354275 Platform: Linux PlatformVersion: 3.10.0-1160.119.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 2) Platform: *CentOS Linux release 7.9.2009 (Core)* 3) uname -a: *Linux fox-c18 3.10.0-1160.119.1.el7.x86_64 #1 SMP Tue Jun 4 14:43:51 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux* 4) recon-all.log: see attached 5) script used: attached (T1_recon_all2.sh) Thank you ! Angelika

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AABC Release 2 of more longitudinal HCP-Aging & AABC Data
by Jennifer Elam 28 Jan '26

28 Jan '26

External Email - Use Caution *AABC Release 2 of more longitudinal HCP-Aging & AABC Data * The Aging Adult Brain Connectome (AABC) consortium is pleased to announce its second release of imaging and non-imaging phenotypic data on the *ConnectomeDB powered by BALSA <https://secure-web.cisco.com/1XxcWoohRobuw1WSCh6edBdaGxyD_rp1GlemcFbF_8jlSX…>* platform. AABC Release 2 includes 632 additional sessions collected on participants from targeted groups newly recruited for AABC and more longitudinal visit data and followups (up to visit 4) from HCP-Aging (HCA) participants. It is inclusive of the previous AABC 1 Release. AABC is a longitudinal follow-on study to the HCA study of typically aging participants ages 36-90+. AABC has recruited ~950 participants (legacy HCA and new) for two additional longitudinal visits, collecting up to four timepoints per participant to generate within-participant brain trajectories over spans of up to 10 years, enabling examination of vulnerability and resilience factors related to cognitive decline. AABC Release 2 includes cross-sectional (V1) and longitudinal (V2, V3, V4) 3T MR scans and non-imaging phenotypic data from 1396 typically aging adults (ages 36-90+) in the *HCP-Aging* and *AABC* projects. This includes data for 1396 V1, 915 V2, 471 V3, and 96 V4 sessions (total = 2878). It includes preprocessed and unprocessed imaging data for all included modalities (structural, high-res hippocampal T2 [unprocessed only], resting state fMRI, task fMRI, diffusion, and ASL) from 1390 participants in 2789 imaging visits. It also contains non-imaging data collected over a broad range of domains at imaging visits and in remote follow up surveys (non-imaging events). See *session breakdowns by study and visit/event <https://secure-web.cisco.com/1Ofguj5c8lU0m74FZoyTK636BZvRWBKivB_ywzv82i4vra…>* . *Release 2 Highlights:* - Preprocessed and unprocessed structural MRI, resting state fMRI, task fMRI, diffusion MRI, ASL, and high-res hippocampal T2 [unprocessed only] data in modality-specific "HCP package" datasets downloadable from BALSA (see below). - Most users should access *Preprocessed Recommended *fMRI data that have been cleaned of spatially and temporally specific structured noise and precisely aligned across subjects by multimodal cortical surface registration (MSMAll) using HCP pipelines <https://secure-web.cisco.com/1aacJvW1mdHImrMoNlsjQrehkTIWQkvMzctNAfsV9nqCzE…> that have been developed specifically for HCP-style data. - 3T Multi-modal Imaging Derived Phenotypes (IDPs) for released participant sessions available in CSV (zip archives in IDPs tab) and Connectome Workbench-compatible CIFTI imaging package formats. - 7 T Magnetic Resonance Spectroscopy (MRS) brain metabolite data are available for 282 participant visits. - Non-imaging behavioral and biomeasure data available for released participant sessions and follow up events. - Core Variables, high interest primary variables and summary scores, including MRS brain metabolites, can be viewed and filtered in the BALSA UI (use Column Selector to add, Export CSV to download all Core Variables or selected subset). - >3,000 Extended (XL) variables, including item-level and follow up event variables, for all participant events available in a comprehensive spreadsheet. See Data Dictionary <https://secure-web.cisco.com/1w4WLQASL7dgUjowrLA8VjSQ7qcqVF_OOAecYbXSr4cxpd…> for descriptions of included variables. - NIH Toolbox raw and score data for in-person visits are available as spreadsheets/zip archive. - Visualization instructions and HCA1798 group average template data for visualizing HCP pipelines output, including IDPs, in Connectome Workbench wb_view. *Get Access and Download the data: *Get started by *Registering for BALSA <https://secure-web.cisco.com/1ABz6nrHeh7ZY5Ld4JgxvDpDxuqcrXwViuNH3SssZ7jJh8…>*, click on the “ConnectomeDB” tab, and agree to the AABC Data Use Terms. An academic, non-profit, or government email address is required to agree to the AABC Data Use Terms and access the data. To download imaging data, you must 1) install *Aspera Connect <https://secure-web.cisco.com/1p324dA-654tn2LU5RMwFk65I2EC6rLjVBaKSkVvXw-xBH…>* (*scroll down to “IBM Aspera client-deployed software” to find Aspera Connect download links*) and 2) an Aspera Connect plugin for your browser (available from Firefox, Chrome, Safari, etc.). Set Preferences>Transfers in Aspera Connect to a directory with sufficient space for large downloads. Use the Column Selector and Export CSV to view, filter on, and download all or subsets of Core Variables for selected subjects. To download the full non-imaging data, click the Files tab and Download under AABC_Release2_Non-imaging_Data-XL.csv. *Join the Community.* If you are actively using HCP data and tools, we encourage you to join and be active in the *HCP-Users Google group <https://secure-web.cisco.com/1j4HC4mBHaSeH8_MLgylhkjZx2ucjxd5dcQPzIN-bPYM-6…>*, so that you can tune in to technical discussions on issues that may be of interest. Once you have joined (posts from nonmembers are moderated to control spam), post questions to *hcp-users(a)humanconnectome.org <hcp-users(a)humanconnectome.org>*. *Share your Analyses.* As you work with AABC data and prepare your work for publication, we encourage you to use *Connectome Workbench <https://secure-web.cisco.com/1UksVOQxCxXN1PSTD8_iZe0FH8nhqNyabpAFfqrgZIUGzw…>* to prepare your figures as scenes and *upload your scenes as a BALSA dataset <https://secure-web.cisco.com/188H9BkiEI_P6I5P_y380WASXc34AB_Sd3NhkG0D6zxkkD…>* that can be linked from your publication. Don’t forget to cite the *HCA and AABC grants <https://secure-web.cisco.com/1RaBEYH46916aUctXV_85CuHdH1TMaqlcjbKYOvFi8x2ZQ…>* and *BALSA <https://secure-web.cisco.com/1Kt_PfcOWm9-dzMelOgh3-pR4S8ZnTQqKtnFPm3gsk8EMQ…>* in your manuscript! *Stay Tuned!* In coming months, we will be working on improvements to ConnectomeDB powered by BALSA to enable additional ways to transfer data via command line and other transfer services we are exploring. We will announce updates on the HCP-Users group! Best, AABC Consortium -- Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience 660 South Euclid Avenue St. Louis, MO 63110 elam(a)wustl.edu http://secure-web.cisco.com/1bLLYhhcdC_J57LMgAzFLkNi-KlCY6dxwIXHFcQbEgJ-ydM…

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