Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30055 discussions

Re: Freesurfer Digest, Vol 256, Issue 4
by Riheb Naili 07 Jun '25

07 Jun '25

External Email - Use Caution Dear FreeSurfer Support Team, I hope this message finds you well. I am currently in the process of installing FreeSurfer for my research work and would like to request a license file in order to complete the installation. Could you please provide me with the necessary license or let me know the steps to obtain it? Thank you very much for your support. Best regards, Le sam. 7 juin 2025 à 02:20, <freesurfer-request(a)nmr.mgh.harvard.edu> a écrit : > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via email, send a message with subject or > body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > Today's Topics: > > 1. Question Regarding Longitudinal vs. Cross-Sectional FreeSurfer > Analysis > (Keller, Lara) > 2. PetSurfer surface-based SUVR (Mia Anthony) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 6 Jun 2025 09:43:35 +0000 > From: "Keller, Lara" <Lara.Keller(a)lvr.de> > Subject: [Freesurfer] Question Regarding Longitudinal vs. > Cross-Sectional FreeSurfer Analysis > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <53e88a0d5d704d97b16fa0e14f362ce9(a)lvr.de> > Content-Type: multipart/alternative; > boundary="_000_53e88a0d5d704d97b16fa0e14f362ce9lvrde_" > > External Email - Use Caution > > Dear FreeSurfer Community, > > > I am currently analyzing structural MRI data using FreeSurfer 8 and have a > specific question regarding the longitudinal pipeline. My dataset consists > of two groups: > > * One group has 3 follow-up timepoints > * The other group has 2 follow-up timepoints > > > I have processed the data using both the cross-sectional and longitudinal > recon-all pipelines, and I am now wondering whether it is appropriate to > proceed with the longitudinal output, despite the unequal number of > timepoints between groups. > > > Key Concerns: > > 1. Since FreeSurfer creates subject-specific within-subject templates, > could the differing number of sessions lead to relevant systematic > differences between the groups? Specifically, will the segmentation > accuracy or signal-to-noise ratio be noticeably different between the > groups due to these variations? > 2. Would it be valid to continue using the longitudinal output but > statistically account for the unequal number of sessions (e.g., via Linear > Mixed Models)? > 3. Alternatively, would it be preferable to use cross-sectional outputs > to avoid potential biases introduced by differing template quality? > 4. If I analyze only one specific timepoint for certain research > questions, should I still use the longitudinal output, or would > cross-sectional data be more appropriate? > > > I find myself torn between the improved segmentation accuracy of the > longitudinal approach and the potential systematic differences introduced > by the varying number of timepoints. Would a viable solution be to proceed > with the longitudinal output while ensuring robustness by replicating key > findings using cross-sectional data? > > > I would greatly appreciate your insights on whether it is methodologically > sound to proceed with the longitudinal pipeline in this case and, if so, > how best to control for the unequal timepoints in statistical analysis. > > > Thank you very much for your time and guidance! > > > Best regards, > > Lara > >

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Re: Freesurfer Digest, Vol 256, Issue 4
by fsbuild 07 Jun '25

07 Jun '25

External Email - Use Caution  You should download and install the latest 8.0.0 installer package matching your machines OS (unless you have previous work you need to continue and/or support that was processed using an older version of Freesurfer).  The table of download links for the 8.0.0 release is here:https://secure-web.cisco.com/1Fv5NKe-WJ3HEIvKFeah03WXMkmxek9CVftoYlMfL… There is a link on that page to “… setup and install notes for 8.X releases …”https://secure-web.cisco.com/14v3LUZSDxyxAotnogEMhXQVJQETg8F-blx28o4LAmRKX_q6CWk4U8-CWEeOdVDSC3laKwG0q6K4ipxWmt9dFiISrsUWdu45X_Aivw_6hQp5JCJ1Y3KRPE9je5X4YV3lig7LPW3NXXtt3Iw1RHwY5WF5sIkpNX0YBKf-0koOlsReokBGKxUSgSVX6L5H7raIwH6zIN8ltXImEp0FJrVSeyuS1grweSurWpnfggbdNk1_gAaBp-lCaHgtwQXxL12ecm21eCjFUBKJGCCUEcNdi7jRuQPaRbt2pCr-ncmF0ZN8-xaITHUEeXaxtb4z8Bn0F/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads%2Frel8notes You can read at the top of that page about where to route to to fill out the form to get a license file emailed to you.  Once you have received the license file, follow the above instructions about how to setup the license file on your machine. - R. On Jun 7, 2025, at 02:34, Riheb Naili <riheb.naili(a)isimg.tn> wrote:        External Email - Use Caution        Dear FreeSurfer Support Team, I hope this message finds you well. I am currently in the process of installing FreeSurfer for my research work and would like to request a license file in order to complete the installation. Could you please provide me with the necessary license or let me know the steps to obtain it? Thank you very much for your support. Best regards,

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Open slots at upcoming FreeSurfer course
by Sennott, Liam Ricker 04 Jun '25

04 Jun '25

Hello all, There are still spots open for the Virtual FreeSurfer course happening next week on June 9th, 10th, and 12th. Please visit our course page to learn more and sign up: https://surfer.nmr.mgh.harvard.edu/fswiki/VirtualCourse We will be accepting new registrations up until the start of the class (Monday, June 9th at 9:00am EDT). However, we will not be providing technical support past 5:00pm EDT on Friday, June 6th. Afterwards, you will need to get the course software set up on your own if you wish to attend. Any question about the course can be sent to fscourse(a)mgb.org<mailto:fscourse@mgb.org>

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03 Jun '25

Dear Freesurfer experts, I would like to register surface data (an 'overlay' file) from fsaverage_sym space back to the subject's native rh.white surface. This seemed to work fine for the lh data using: mri_surf2surf --srcsubject fsaverage_sym --trgsubject fs8 --hemi lh --sval mysurfacedata_lh.gii --tval mysurfacedata_lh_native.mgh However, I am struggling to do this for the right hemisphere. Do you have any recommendations? Thank you in advance, Best, Felix

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Re: recon-all error: SynthStrip process killed on macOS Sequoia 15.5 for subject 100206
by fsbuild 02 Jun '25

02 Jun '25

External Email - Use Caution The path /Applications/Freesurfer/dev/bin in the log indicates a development build is running.  Since that could be unstable, you could try installing and running the 8.0.0 release, https://secure-web.cisco.com/1q_jK67tubl-gK663E2lJ1Cv-nNx2UB7fhRxZMVS2UCp5E… But with either the 8.0.0 release from 2/2025 or subsequent dev builds, the machine may not have the resources to run the new recon-all setup.  MacOS may kill any process that is too greedy for system resources - which is consistent with the message in the log.   The 8.0.0 release and subsequent dev builds requires at least 16G of RAM for recon-all on top of what MacOS plus any other programs are currently using for memory.   That could translate to a minimum of 24G of RAM ; the 8.0.0 release was tested on Macs with not less than 32G RAM with no other applications running. So you could also try reverting to the old recon-all behavior from the 7.X releases by setting the environment variable  FS_V8_XOPTS on the recon-all command line, e.g., $ export FS_V8_XOPTS=0 && recon-all -all -i I50 -s Subj001 - R. On Jun 2, 2025, at 04:53, nil ahmadi <naiaddiamond1998(a)gmail.com> wrote:        External Email - Use Caution        Hello FreeSurfer Developers, I am running FreeSurfer on my MacBook Air with macOS Sequoia Version 15.5 (ARM64 architecture). I am processing subject 100206 using the recon-all pipeline with T1w and T2w images from my data directory located on an external drive. However, during the process, the step involving mri_synthstrip fails with the following error message: mri_synthstrip --threads 1 -i /Volumes/MyDRIVE/freesurfer_output/100206/mri/orig.mgz -o /Volumes/MyDRIVE/freesurfer_output/100206/mri/synthstrip.mgz Configuring model on the CPU Running SynthStrip model version 1 Input image read from: /Volumes/MyDRIVE/freesurfer_output/100206/mri/orig.mgz Processing frame (of 1): 1 Killed After this, the recon-all command exits with errors at Thu May 29 09:27:14 CST 2025. Here are some details about my setup: FreeSurfer version: dev version built May 26 2025 (freesurfer-macOS-darwin_arm64-dev-20250526-d84643b) Platform: macOS Sequoia Version 15.5 running on Apple Silicon (ARM64) Hardware: MacBook Air (Apple M3) Data location: External drive mounted at /Volumes/MyDRIVE with sufficient free space (4.4 TiB available) Memory status: System has some paging/swapping activity (vm_stat output attached) I have attached the recon-all.log file from Could you please advise on how to resolve this SynthStrip “Killed” error?  Any suggestions on running FreeSurfer successfully on macOS 15.5 with Apple Silicon would be greatly appreciated. Thank you very much for your support. Best regards, Niloufar Ahmadi

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Guidance on ADC Value Extraction and Rescaling Factor
by Taghizadeh Mortezaei, Nima 01 Jun '25

01 Jun '25

Hello everyone, I am currently working with ADC values extracted from inhomogeneity bias-corrected ADC MRIs obtained through SAMSEG and have encountered a few issues that I would greatly appreciate your insights on. 1. Units for ADC Values: When extracting ADC values for my ROIs, using 3D Slicer, I noticed that no unit was provided for the ADC values, neither in the software nor in the imaging visualization tools (PACS, VISAGE). I also checked the DICOM metadata for ADC and DWI MRIs but could not find any relevant tags related to ADC values, rescaling, or intersection. As a result, I am uncertain about the unit or scale used for the ADC values. 2. Discrepancy in ADC Value Range: The mean ADC values extracted from the bias-corrected image for my ROIs were in the range of 150-250. These values seem far away from the normal average ADC values for these structures. I suspected that the bias correction might have influenced these values, so I also extracted the values from the original ADC image. In this case, the values ranged from 1200-1500 for ROIs. However, I still could not identify any unit or rescaling factor. Considering that the average normal ADC values for my ROI are around 1000 to 1500 x 10-6 mm²/s, I have two questions: For extracting radiomics features (including ADC values) from the ADC image, would you recommend using the bias-corrected image or the original ADC image as the scalar volume? Based on the values I found, there must be a rescaling factor (like 10-6). Would you happen to know where I might find the rescaling factor, or how I could confirm it? I would greatly appreciate any guidance you could provide on these issues. Thanks, Nima

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Clarification on Label 24 – CSF in FreeSurfer
by Emma Rodrigues 01 Jun '25

01 Jun '25

External Email - Use Caution Dear FreeSurfer Experts, I hope this email finds you well. I'm reaching out to request clarification regarding label 24 – CSF in the FreeSurfer software. From my observations, this label appears to correspond to a region near the third ventricle. However, it does not seem to be included in any of the standard ventricular volume measurements. Additionally, I’ve noticed that in segmentations produced with SynthSeg, label 24 – CSF appears to correspond to the subarachnoid space, which adds some confusion. I’ve looked for documentation or forum discussions on this topic but have encountered mixed information. Could you please clarify what anatomical region label 24 – CSF represents in the original (pre-SynthSeg) version of FreeSurfer? Thank you in advance for your time and help. Best regards, Emma Rodrigues

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Opportunity to contribute to BRIDGE project
by Joana Braga Pereira 27 May '25

27 May '25

External Email - Use Caution Dear all, Please find an exciting opportunity below. For further information and queries please do not hesitate to contact Matthew (in CC: mathew(a)incf.org) ***About the Project*** The BRIDGE project (braindatagovernance.org <https://secure-web.cisco.com/1jTqF6FToUlilGFw1NR0zphQrV_aicG82sl_532pbnRBqZ…>), is tasked to develop international data governance frameworks (IDGFs) to facilitate the cross-border sharing of brain and mental health data, addressing the unique challenges posed by varying legal, ethical, and technical landscapes. It is well known that data accessibility, awareness, and training resources are far more prevalent in high-resource settings, leaving low- and middle-income countries at a disadvantage. This imbalance significantly hampers the global equity and inclusiveness of neuroscience research, particularly in mental health. To effectively address and minimize this disparity, BRIDGE is working to identify and thoroughly understand the barriers that exist at each stage of the research process across high-, middle-, and low-resource settings. For the Pathfinders Phase Two component of the project, volunteers will be asked to access several datasets (2-4) from different parts of the world and record the steps of downloading, minimally processing and analyzing each dataset.* All volunteers who complete the steps for their assigned datasets will be offered co-authorship on any subsequent manuscripts produced from their efforts.* In the coming weeks we will be ready to launch this phase of the BRIDGE project. We would like to enlist PhD students and Postdocs who have had previous experience handling human brain data to volunteer with us. All work can be completed remotely. Thank You! *Sign up here:* BRIDGE Pathfinders Sign Up <https://secure-web.cisco.com/15S3CEFy9BYdILHaaIpJeDfjDEOk6sCoiFJQ8UZ08hVw5U…> -- Mathew Birdsall Abrams, PhD, MPH Director, Science and Training International Neuroinformatics Coordinating Facility Karolinska Institutet Nobels väg 15A SE-171 77 Sweden http://secure-web.cisco.com/1tA9CkZljq16-3xGKhpKZxhmE-bbjYthPUNQkWo7vGrtqAH… <https://secure-web.cisco.com/1Hl7aMSAc1sAxUQXCzDfC2Oo6Pjf2ySDEw_3gq3Ny7gpv0…>

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Re: [Freesurfer] Question on using thalseg_1.1.h5
by Georgios Argyropoulos 23 May '25

23 May '25

External Email - Use Caution Many thanks and apologies, Henry - I figured it out... I stupidly replaced your improved segmentation script in both the scripts and the bin directory instead of only replacing the former. many thanks for your time, much appreciated g

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June 2025 FreeSurfer course
by Sennott, Liam Ricker 21 May '25

21 May '25

Hello all, The next virtual FreeSurfer course will be held on June 9th, 10th, and 12th. Registration for this virtual FreeSurfer course is opening on Wednesday, May 21st at 10am Eastern Daylight Time. Visit our course website to find out more information: https://surfer.nmr.mgh.harvard.edu/fswiki/VirtualCourse Specific questions about the course can be sent to fscourse(a)mgb.org<mailto:fscourse@mgb.org>

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