Freesurfer May 2025

freesurfer@nmr.mgh.harvard.edu

21 participants
24 discussions

longitudinal analysis on one subject
by Isabella Rossellini 13 Jul '25

13 Jul '25

External Email - Use Caution Hello Freesurfer users/experts, I am working with Freesurfer 7.4.1 on a MacStudio (macOS 15.2) and I would like to ask your opinion about the following. Basically, we had an anxiety treatment study and I would like to analyze one subject who has 5-time points (0, 3, 6, 9, 12) with a longitudinal pipeline, two-stage model. Is it possible to run this on one person only and see the changes between these time points? I have never done this before on one subject so I am not sure what the best approach would be to look at the changes. After running the longitudinal preprocessing (base, long), should I generate the tables of freesurfer parcellation/segmentation stats data (aparcstats2table, asegstats2table)? Or can I just follow the two stage model steps? Maybe glm only works on a group of subjects. https://secure-web.cisco.com/1iC7gpXrtEAUPrcmI22C302poe7thUhcUmsjgK95UydNOq… (We have 9 more subjects - 10 in total - so I was hoping to visualize the pattern of changes one by one, in each subject, since these patients showed different changes in anxiety based on self-reported questionnaires) Sincerely, Isa Rosselini

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Updates/bug fixes available for the 8.0.0 release
by fsbuild 27 Jun '25

27 Jun '25

External Email - Use Caution Some updates/bug fixes are available for an existing installation of the Freesurfer 8.0.0 release.  The list of files you can update along with a brief comment about the change(s) are: $FREESURFER_HOME/bin/csvprintScript changed to use python3 - values for eTIV should no longer be misreported as 0.00 for data processed with the recon-all command $FREESURFER_HOME/bin/recon-allFixes for options -autorecon1, -nonuintensitycor.  Add flag -no-fix-ga to turn off fixing of gyrus ambiens part of the cortex label. $FREESURFER_HOME/bin/gtmseggtmseg now uses samseg by default $FREESURFERR_HOME/bin/xhemiregModifications to make xhemireg work with 8.0. $FREESURFER_HOME/bin/xcerebralseggtmseg now uses samseg by default $FREESURFER_HOME/bin/post-recon-allgtmseg now uses samseg by default $FREESURFER_HOME/python/packages/gems/SamsegLongitudinal.pyfix parameters to surfa.image.transform() $FREESURFER_HOME/etc/recon-config.yaml Added option -no-fix-ga to turn off fixing of gyrus ambiens part of the cortex label. Please note THESE UPDATES DO NOT CHANGE THE OUTPUT OF THE recon-all COMMAND. If these updates are of interest to you, then please go the 8.0.0 download URL,https://secure-web.cisco.com/15mh8yOb2RWi2iQyUfX1LgM0gB5PobUejtWnQDIeOm… and download the fs8_update.sh script. On MacOS run the script as follows,$ sudo FREESURFER_HOME=/Applications/freesurfer/8.0.0  bash  fs8_updates..sh On CentOS and Rocky8 Linux run the script as follows,$ sudo FREESURFER_HOME=/usr/local/freesurfer/8.0.0-1  bash  fs8_updates.sh On Ubuntu Linux run the scripts as follows,$ sudo FREESURFER_HOME=/usr/local/freesurfer/8.0.0  bash  fs8_updates.sh You will be prompted on the command line as to whether or not you want to install each file, including displaying the description of the change(s) listed above.

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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

2 5

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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Re: [Freesurfer] Freesurfer 8 + PetSurfer talairach.m3z
by Simon Jones 18 May '25

18 May '25

External Email - Use Caution OK, thank you Yujing I'll see if we can update the installation Simon

2 1

Freesurfer 8 + PetSurfer talairach.m3z
by Simon Jones 16 May '25

16 May '25

External Email - Use Caution Dear FS I tried to perform PetSurfer following recon-all pipeline using FreeSurfer 8. When I run gtmseg -s $sub I get error ERROR: cannot find talairach.m3z I was able to create the file talairach.m3z which is omitted from version 8 recon-all pipeline using mri_ca_register but I guess I should be converting the files in the subject/mri/transforms/synthmorph.1.0mm.1.0mm directory into talairach.m3z using mri_warp_convert. Is there an example of how to do that or are some other steps recommended? Thanks, Simon

2 1

mri segstats "masksign abs" syntaxis option
by Gonzalo Rojas Costa 15 May '25

15 May '25

External Email - Use Caution Hi: Using "--masksign abs" option: which must be the syntax for "--maskthresh" option in mri_segstats command? Sincerely, Gonzalo M. Rojas-Costa Adjunct Assistant Professor School of Medicine Finis Terrae University Santiago Chile

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Freesurfer May 2025