Freesurfer July 2025

freesurfer@nmr.mgh.harvard.edu

42 participants
63 discussions

TRACULA statistics - len_center issue
by Gabriella Monopoli 21 Jul '25

21 Jul '25

External Email - Use Caution Dear experts, I analyzed a few subjects from my dataset using TRACULA (FreeSurfer version 8). While examining the pathstats.overall.txt file for the left anterior longitudinal fasciculus, I noticed an anomaly: the Len_Center value is greater than Len_max. This occurs for all the subjects analyzed and also appears in other tracts. I was wondering whether this issue might be related to my data, a bug in the anlysis, or perhaps it's not actually an error at all. I'm sure you'll be able to help me understand how to resolve this and properly analyze my data. I've attached, as example, the pathstats.overall.txt file of one of my subjects. Best regards, Gabriella

1 0

2D vs 3D gradient distortion correction (mri_gradunwarp)
by Annchen Knodt 20 Jul '25

20 Jul '25

External Email - Use Caution I have a longitudinal dataset collected on a Siemens Skyra, where online distortion correction on the T1s was turned OFF for the first wave several years ago, and with an upgrade to XA30 since then, it is now turned ON for the second wave of data collection and performing a 2D (in-plane) correction. Obviously, we want the acquisitions to match as closely as possible between the two timepoints, so I am trying to figure out how to use gradunwarp to perform post-hoc correction on the first scans. A problem I am running into (see my thread on HCP’s gradunwarp github page<https://secure-web.cisco.com/1UEsGaoLMJInc49tXx1leDHidHoj0m6ydT6viNz9VH1gN5…>) is that the software performs a 3D correction, which is not the same as the 2D correction being applied to my wave 2 data. I don’t yet know of a way to either: 1. apply just a 2D correction to my wave 1 uncorrected data to match what the scanner is doing at wave 2 (I’ve communicated with a Siemens rep who says there is no documentation he can share on the 2D correction to help me figure out how to do this) or 2. UNDO the 2D correction on my wave 2 data, so that I can then use gradunwarp to apply the 3D correction to both waves. I don’t have a very good understanding of the differences between the 2D and 3D corrections, and I do not currently have a dataset with both uncorrected and 2D-corrected copies of the same scan to allow me to experiment with and test various strategies (hoping to get this soon, but not sure when I’ll be able to). As such, I am hoping that someone with more experience or knowledge on this might be able to shed some light on the nature of the issue and severity of the problem and/or offer guidance on how I might be able to correct it. Thanks! Annchen

2 1

Re: Freesurfer output. Segmentation fault (core dumped) during parcellation step
by fsbuild 18 Jul '25

18 Jul '25

External Email - Use Caution This posting indicates that changing the path to ./stats from ../stats got rid of a segmentation fault.  I would at least check that all paths in the arguments ro mris_anatomical_stats are correct though. https://secure-web.cisco.com/17sKLSeDVET5-5S3ZEgRGL6lX55gFUMqV2UWISNObj-rC9… But I don’t see the error in the recon -all log you sent which is apparently from May 2020 showing Freesurfer 6.0.0 is being run on RedHat Enterprise Linux 7.5. - R. On Jul 10, 2025, at 16:24, Samantha Hendry <shendry2(a)ed.ac.uk> wrote:mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab FMS_0094 lh white

3 3

FreeSurfer license request
by 李昊宇 18 Jul '25

18 Jul '25

External Email - Use Caution Dear FreeSurfer team, I would like to obtain a FreeSurfer license for academic research use. Due to the registration page can't run properly and gives the 'FreeSurfer Registration Error reCAPTCHA not checked' error message, I wrote this email to request for a license file. Here are the required details: First Name: Haoyu Last Name: Li Institution: Shanghai Jiao Tong University Type of institution which will use this software: Non-profit education/research email: haoyu_li(a)sjtu.edu.cn Telephone: +86 19817863375 Operating System/Platform: Linux Number of Users: 1 Please send the license file to this email address. Thank you very much! Best regards, Haoyu Li

2 1

Fwd: Make Docker of FreeSurfer Dev version.
by fsbuild 18 Jul '25

18 Jul '25

External Email - Use Caution We do not support end users building freesurfer from source.   Development builds can be unstable and may not work and/or work the same way depending upon when you download them; the same is true for checking out the source code on any given day. You should instead create a docker container running a standard Ubuntu 22 release, e.g., LTS 22.0.4, for which there already exists a .deb installer package corresponding to a stable freesurfer release.   The freesurfer releases are listed here with the latest release being 8.0.0, https://secure-web.cisco.com/1xCL7oeqhtHSjdQttn-ynKQW05sIF78iIeQcw7h6OTSotE… Install a freesurfer Ubuntu 22 .deb package in the container using the standard install command, e.g., if you download the 8.0.0 release installer,https://secure-web.cisco.com/16l9n1feB3EbaBIKS8nXkmTUTR-uy0sofOYG… then the install command would be,$ sudo apt install freesurfer_ubuntu22-8.0.0_amd64.deb - R.

1 0

Re: FreeSurfer license request
by fsbuild 18 Jul '25

18 Jul '25

External Email - Use Caution There is likely some javascript not loading in your browser preventing something like captcha graphics from displaying.  Check to make sure the browser is not blocking any javascript and/or try a different browser.   Part of filling out the form and registering includes using the mouse or pointing device to click on and accept the terms of the displayed license agreement.   We do not distribute licenses via email since that would bypass the legal consent step. - R. On Jul 18, 2025, at 03:28, 李昊宇 <haoyu_li(a)sjtu.edu.cn> wrote:       External Email - Use Caution         Dear FreeSurfer team, I would like to obtain a FreeSurfer license for academic research use. Due to the registration page can't run properly and gives the 'FreeSurfer Registration Error reCAPTCHA not checked' error message, I wrote this email to request for a license file. Here are the required details: First Name: Haoyu Last Name: Li Institution: Shanghai Jiao Tong University Type of institution which will use this software: Non-profit education/research email: haoyu_li(a)sjtu.edu.cn Telephone: +86 19817863375 Operating System/Platform: Linux Number of Users: 1 Please send the license file to this email address. Thank you very much! Best regards, Haoyu Li _______________________________________________ Freesurfer mailing list -- freesurfer(a)nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1n8TEBGY47Kdny8w5LiDfbzot98S-MbfB_DPUMKIAPfRl_…

1 0

Make Docker of FreeSurfer Dev version.
by Óscar Peña-Nogales 18 Jul '25

18 Jul '25

External Email - Use Caution Dear, I'm attempting to create a *docker version of the FreeSurfer Development version* following the steps shown in https://secure-web.cisco.com/1zahxQetlgW4KiuOIq4HdcILTBQvomXB-frywITaD7T90r… Nevertheless, I'm encountering some issues, probably related to how I set up the docker, but they are blocking me. I attach the Dockerfile I'm trying to make (up to the step where it fails). The error raised by the make command is: *[ 57%] Building CXX object mris_convert/CMakeFiles/mris_convert.dir/mris_convert.cpp.oIn file included from /usr/include/ITK-5.2/gifti_io.h:4, from /root/freesurfer/include/gifti.h:26, from /root/freesurfer/mris_convert/mris_convert.cpp:40:/usr/include/ITK-5.2/itk_zlib.h:33: error: "ITK_USE_SYSTEM_ZLIB" redefined [-Werror] 33 | #define ITK_USE_SYSTEM_ZLIB | <command-line>: note: this is the location of the previous definitioncc1plus: all warnings being treated as errorsmake[2]: *** [mris_convert/CMakeFiles/mris_convert.dir/build.make:80: mris_convert/CMakeFiles/mris_convert.dir/mris_convert.cpp.o] Error 1make[1]: *** [CMakeFiles/Makefile2:10396: mris_convert/CMakeFiles/mris_convert.dir/all] Error 2make: *** [Makefile:146: all] Error 2* Last, see I'm interested in making the docker base image in Ubuntu 22.04. Thanks in advance, Óscar

1 0

Info about Cortical Parcellation Participants?
by Jamie Hanson 14 Jul '25

14 Jul '25

External Email - Use Caution Hello Freesurfer list- I had a (hopefully) quick question about the cortical parcellation manual labeling data... specifically, is there any information about race/ethnicity and education levels for these participants? It looks like from some past replies (in ~2009), the cortical labels were based on two sets-- one done by Rahul Desikan (~40 subjects) and the other by Christophe Destrieux (~24 subjects). I'm presuming it is these two papers: -Desikan, R. S., Ségonne, F., Fischl, B., Quinn, B. T., Dickerson, B. C., Blacker, D., ... & Killiany, R. J. (2006). An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest. Neuroimage, 31(3), 968-980. -Destrieux, C., Fischl, B., Dale, A., & Halgren, E. (2010). Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature. Neuroimage, 53(1), 1-15. If that's correct, those publications only list a bit about the participants' ages and sex. There's nothing about these other demographic factors, and I thought I would try to track that information. Thanks much in advance for the help, and all the best, Jamie. --- Jamie Hanson Associate Professor, Psychology Research Scientist, Learning Research and Development Center University of Pittsburgh

1 1

Control Points Not Taken Into Account
by Singh, Karan 14 Jul '25

14 Jul '25

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to add control points where there is white matter, specifically in the left temporal lobe. I have saved the control points as "control.dat" and saved it in the subject's "tmp" folder. However, even when I re-run the recon code and open Freeview, it still doesn't take my control points into account. There is no error message either; it always says "Completed without error" whenever I re-run the code. I have attached a screenshot of the error regarding the control points. 1). FreeSurfer version: freesurfer-linux-ubuntu18_x86_64-8.0.0-20250204-0f2bd3a 2.) Platform: Linux PlatformVersion: 5.4.0-150-generic 4.) recon-all.log: see attached Sincerely, Karan Singh The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

1 0

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

2 7

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer July 2025