Freesurfer

freesurfer@nmr.mgh.harvard.edu

4 participants
30076 discussions

Support regarding QDEC
by Henry Do 23 Dec '25

23 Dec '25

External Email - Use Caution Hi freesurfer experts, I am working on a project, and I have used mri_glmfit to compare the cortical thickness of the patient cohort with that of the control. When I examined the results, I noticed some unexpected clusters of atrophy and wanted to investigate which subjects contributed to each cluster. In the previous version, I could do this easily with QDEC, but unfortunately, my current computer can’t set up QDEC because the Windows version is not compatible with FreeSurfer 6.0. I hope you can help me with an alternative method for performing this analysis, as it would be greatly beneficial for my project. Sincerely, Henry Hiệp ĐỖ (Henry DO) Tran Minh Hiep DO (Henry DO) PhD Candidate | B.Biomed.Eng Faculty of Science, School of Psychology THE UNIVERSITY OF SYDNEY FRONTIER Frontotemporal Dementia Research Group | Brain and Mind Centre | M02G | Level 1, 94 Mallet Street | Camperdown | NSW | 2050 Contact: +61 451 973 339 Email: trdo0838(a)sydney.edu.au<mailto:trdo0838@sydney.edu.au>

2 1

7.2.0 -notal-check talairach.xfm relevant beyond eTIV?
by Dr. Cornelius Kronlage 23 Dec '25

23 Dec '25

External Email - Use Caution Dear freesurfer team, using freesurfer 7.2.0, recon-all fails for some subjects in a certain dataset (denoised MP2RAGEs) for me at this stage: #@# Talairach Failure Detection Wed Dec 10 11:30:01 GMT 2025 /data/output/fs_outputs/sub-007/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0056, pval=0.0000 < threshold=0.0050) Command exited with non-zero status 1 The talairach.xfm registration indeed looks completely off. However, if I use "-notal-check", recon-all runs through with outputs (surfaces etc.) that look fine. It seems like the talairach.lta created by mri_em_register a couple of steps later is correct and downstream steps use this. The incorrect talairach.xfm only appears to have have an impact on the eTIV estimation (not so relevant for me). Is it appropriate to run recon-all with -notal-check with an incorrect talairach.xfm but an accurate talairach.lta - or are there other issues this might cause? Thank you and best wishes, Cornelius

2 1

mri_gtmpvc error in version 8.1 - missing segmentation ids
by Daniel Gutstein 23 Dec '25

23 Dec '25

External Email - Use Caution Hello, I am encountering an issue when running mri_gtmpvc in Freesurfer 8.1.0. It fails with the following "ERROR: scale reference id 174 cannot be found in seg id list". Upon inspecting gtmseg.ctab, seg id 174 (pons) is missing in version 8.1 while this was present in version 7.x. Several other segmentation ids are also inconsistent between version 7 and 8. Could you please clarify whether mri_gtmpvc is fully compatible with the updated segmentation FreeSurfer 8.1, and whether there is a recommended workflow? Below is the full command and output: ---------- mri_gtmpvc --i pet/S09/PET.nii.gz --o pet/S09/gtmpvc --reg-identity --mask S09/mri/brainmask.mgz --psf 3.0 --mg 0.20 2 41 --seg S09/mri/gtmseg.mgz Loading input pet/S09/PET.nii.gz done loading input 1 frames Using identity registration 8.1.0 mri_gtmpvc --i pet/S09/PET.nii.gz --o pet/S09/gtmpvc --reg-identity --mask S09/mri/brainmask.mgz --psf 3.0 --mg 0.20 2 41 --seg S09/mri/gtmseg.mgz vgthresh 0.001000 nReplace 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 256 avail.processors, using 1 Creating output directory pet/S09/gtmpvc Loading seg for gtm S09/mri/gtmseg.mgz Loading seg ctab S09/mri/gtmseg.ctab Reading S09/mri/gtmseg.lta Pruning ctab tissue type schema Checking tissue type done with seg vol maxFWHM = 3 (voxels), PadThresh=0.0001, nPad=10 Loading mask S09/mri/brainmask.mgz Automask, reducing FOV 1 region 256 256 256 reduced to 56 25 23 140 149 180 Data load time 10.2 sec nmask = 1646176, nsegs = 101, excluding segid=0 FWHM: 3 3 3 Std: 1.27398 1.27398 1.27398 nPad 10, PadThresh 0.0001 Checking Ref Ids ERROR: scale reference id 174 cannot be found in seg id list ---------- Thank you. Daniel Gutstein Research Data Analyst Senior Northwestern University | Mesulam Institute for Cognitive Neurology & Alzheimer's Disease 300 E. Superior Street | Tarry 8-734 | Chicago, IL 60611 daniel.gutstein(a)northwestern.edu<mailto:daniel.gutstein@northwestern.edu> | (312) 503 - 8150

2 1

wm edits, fs8.0.0: rerunning leaves wm-surfs unchanged
by Zahnert, Felix 23 Dec '25

23 Dec '25

Dear experts, I have run recon-all using Freesurfer 8.0.0 and corrected wm.mgz in some subjects (deleting voxels where ?h.white grossly extended into gm by assigning them values of 1; adding voxels where juxtacortical hypointensities were misclassified as gm by assigning them 255). After these edits (and saving wm.mgz), I ran recon-all -s <subject> -autorecon2-wm -autorecon3. However, this left the reconstructed surfaces virtually unchanged. Even areas of larger edits are left unchanged. I did check for small areas of stray voxels that could have led to such misclassification. In the documentation, it is recommended to run recon-all with the -make flag in such cases, which no longer seem to be supported. Do you have any recommendations? Thank you so much, Best, Felix

3 7

(无主题)
by m15178125606 22 Dec '25

22 Dec '25

External Email - Use Caution confirm8ab604b7c10759a86abf9caa297c113d800ff2d7

1 0

Fw:Welcome to the "Freesurfer" mailing list
by 杜文杰 21 Dec '25

21 Dec '25

External Email - Use Caution 杜文杰 251300255(a)st.usst.edu.cn Forwarded message: From：freesurfer-request<freesurfer-request(a)nmr.mgh.harvard.edu>Date：2025-12-22 12:25:17(中国 (GMT+08:00))To：251300255<251300255(a)st.usst.edu.cn>Cc：Subject：Welcome to the "Freesurfer" mailing listWelcome to the "Freesurfer" mailing list! To post to this list, send your message to: freesurfer(a)nmr.mgh.harvard.edu You can unsubscribe or make adjustments to your options via email by sending a message to: freesurfer-request(a)nmr.mgh.harvard.edu with the word 'help' in the subject or body (don't include the quotes), and you will get back a message with instructions. You will need your password to change your options, but for security purposes, this password is not included here. If you have forgotten your password you will need to reset it via the web UI. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1nbhTglPHEWpxskmpl1j9uJdZLKzEP0NJ39X1S2NTtNvDK… <https://secure-web.cisco.com/1nbhTglPHEWpxskmpl1j9uJdZLKzEP0NJ39X1S2NTtNvDK…> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

1 0

skull-stripped images in longitudinal pipeline
by Marco Ganzetti 16 Dec '25

16 Dec '25

External Email - Use Caution Hello, I would like to ask whether providing skull-stripped images as input to the FreeSurfer longitudinal pipeline is appropriate for estimating regional atrophy rates. In particular, are there any drawbacks or limitations when generating the within-subject template if skull-stripped images are used instead of the original T1-weighted images? Best regards, Marco

1 0

Dimension mismatch in bvec & bval
by Ramesh Babu 15 Dec '25

15 Dec '25

External Email - Use Caution Hello, I am frequently facing this issue in the dt-recon process. I used dcm2niix to convert the dicom files. Now I facing an issue Loading BValues from /mnt/conn_analysis/sr_projects_dti/subjects/subj001/dti/subj001_dti.bvec.fixed2 Found 99 bvalues Loading BVectors from /mnt/conn_analysis/sr_projects_dti/subjects/subj001/dti/subj001_dti.bval.fixed2 Found 11 bvectors Detected BVec file as FSL formatted ERROR: DTIstructFromBFiles(): dimension mismatch /mnt/conn_analysis/sr_projects_dti/subjects/subj001/dti/subj001_dti.bvec.fixed2 has 99 rows, /mnt/conn_analysis/sr_projects_dti/subjects/subj001/dti/subj001_dti.bval.fixed2 has 11 rows $ awk '{print NF; exit}' subj001_dti.bval 33 $ awk '{print NF; exit}' subj001_dti.bvec 33 Could you please provide some suggestions? Regards Ramesh

2 2

Open Postdoctoral Scholar (Bronte-Stewart Lab @Stanford University) - Neurology
by Kevin Bryant Wilkins 12 Dec '25

12 Dec '25

External Email - Use Caution The Human Motor Control and Neuromodulation Lab under Dr. Bronte-Stewart<https://secure-web.cisco.com/1pOUryuu1WsebjhWjk0I_OJDZZH2Ocigv6sCRXC_gFJOf3…>, part of the Stanford Movement disorders Center within the Department of Neurology and Neurological Sciences at Stanford University’s School of Medicine, is seeking a postdoctoral scholar to aid in a pilot clinical trial using a novel deep brain stimulation approach for cognitive and cognitive-motor dysfunction in Parkinson’s disease. The goal of the research in the laboratory is to understand the pathophysiology of movement disorders such as Parkinson’s disease. At Stanford, innovations in neural interface technology have allowed us to discover how abnormal electrical brain activity contributes to disorders in movement. In the Human Motor Control and Neuromodulation Lab, the first decoding of electrical activity in deep brain structures during abnormal movement in Parkinson’s disease patients was performed using novel and investigative sensing neurostimulators. Our team has deconstructed brain activity to discover both the neural code responsible and kinematic quantification for various motor symptoms in Parkinson’s disease. This has enabled us to reverse engineer brain circuitry and restore movement in Parkinson’s disease using the first closed loop, demand-based brain pacemakers that respond to neural and kinematic markers of movement impairment. We are now working towards expanding this approach to address the currently unsolved problem of cognitive impairment in Parkinson’s disease. The aim of the current work is stabilizing cognitive and cognitive-motor impairment in Parkinson’s disease using a novel deep brain stimulation approach in an ongoing pilot clinical trial. The current project uses structural neuroimaging to guide DBS lead placement and optimal DBS settings, as well as kinematic analysis of behavioral motor tasks. Additional projects include the development of a remote monitoring tool for Parkinson’s disease and other disorders which recently received FDA Breakthrough Device Designation, as well as continued work related to adaptive (closed-loop) deep brain stimulation for motor symptoms in Parkinson’s disease. The current position offers an exceptional opportunity for a motivated and intellectually curious individual to participate in rewarding and cutting-edge research in human motor control and neurophysiology in Parkinson’s disease. There are also additional exploratory projects in the areas of traumatic brain injury, concussion in athletics, Alzheimer’s disease, Major Depressive Disorder, and Dementia with Lewy Bodies. The desired candidate would have a PhD in Neuroscience, Biomedical Engineering, or a related discipline with experience in structural imaging, electrophysiology (LFP, ECoG, EEG, etc.), motor control and/or cognition. Preferred start date is early 2026. Job Requirements Required: PhD in Neuroscience, Biomedical Engineering or related disciplines with expertise in data sciences Experience in structural imaging (tractography, voxel-based morphometry, etc.) Experience working in the area of motor control and cognition Comfortable analyzing data in Matlab, Python, or similar languages Ability to work well in a diverse team Effective oral and written communication skills Excellent organization skills and demonstrated ability to complete detailed work accurately Excellent problem-solving ability Preferred: Experience with Parkinson’s disease or other clinical populations Experience with deep brain stimulation modeling (volumes of tissue activated, etc.) How to Apply: Apply by sending the following to Kevin Wilkins<mailto:wilkins2@stanford.edu> (wilkins2(a)stanford.edu) CV Cover letter describing interest and relevant experience for the project Three potential reference contacts

1 0

15 PhD positions in the BRIDGE-AI Doctoral Network
by Koen Van Leemput 11 Dec '25

11 Dec '25

External Email - Use Caution Are you passionate about pushing the limits of AI in neuroscience, and eager to make a real-world clinical impact? The BRIDGE-AI Doctoral Network is recruiting 15 fully-funded PhD candidates across Europe to advance trustworthy AI for longitudinal neuroimaging, improving the way neurological diseases are monitored over time: - Deep collaboration between hospitals, universities & industry - Training events in leading European innovation hubs - Ample clinical neuroimaging data and expert guidance - A competitive salary while you research. Apply by 30 Jan 2026 (but applying earlier increases your chances!) Learn more & apply: https://secure-web.cisco.com/1afWJl_-yY2w_KUEtwEGKkPJ9mklhrisjtZuwGPV0nCOus…

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer