Freesurfer December 2025

freesurfer@nmr.mgh.harvard.edu

26 participants
32 discussions

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

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(无主题)
by m15178125606 22 Dec '25

22 Dec '25

External Email - Use Caution confirm8ab604b7c10759a86abf9caa297c113d800ff2d7

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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.

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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

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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

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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

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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…

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DTI Registration issue
by Ramesh Babu 10 Dec '25

10 Dec '25

External Email - Use Caution Hello, I am analyzing my DTI scans in Ubuntu 22 LTS with FreeSurfer 8.1. I am facing a registration issue when I run the following script. # Setting Up Environment BASE_DIR="/mnt/data_analysis/freesurfer_data/sr_dti_analysis/subj02" SUBJECTS_DIR="$BASE_DIR" SUBJECT="subj02_fs" export SUBJECTS_DIR SUBJECT # Define Input and Output Subfolders T1_DICOM="$BASE_DIR/t1_SPGR" DTI_DICOM="$BASE_DIR/epi_dti" T1_NIFTI="$BASE_DIR/t1_nifti" DTI_NIFTI="$BASE_DIR/dti_nifti" DTI_DIR="$BASE_DIR/$SUBJECT/dtrecon" MRI_DIR="${SUBJECTS_DIR}/${SUBJECT}/mri" OUTDIR="$DTI_DIR" # Resampling subject's wmparc, aparc+aseg, and brain volumes to diffusion space for vol in wmparc aparc+aseg brain; do vol_file="${SUBJECTS_DIR}/${SUBJECT}/mri/${vol}.mgz" vol2diff="${OUTDIR}/${vol}2diff.mgz" cmd=(mri_vol2vol --mov "${OUTDIR}/lowb.nii" \ --targ "$vol_file" \ --inv \ --interp nearest \ --o "$vol2diff" \ --reg "${OUTDIR}/register.dat" \ --no-save-reg) echo "${cmd[@]}" "${cmd[@]}" done # Mask FA, ADC, ICV volumes using wmparc2diff.mgz for vol in fa adc ivc; do cmd=(mri_mask "${OUTDIR}/${vol}.nii" \ "${SUBJECTS_DIR}/${SUBJECT}/mri/wmparc2diff.mgz" \ "${OUTDIR}/${vol}-masked.mgz") echo "${cmd[@]}" "${cmd[@]}" done # Resampling masked volumes to MNI space interp="trilin" template="$FREESURFER_HOME/average/mni152/mri/brain.mgz" # MNI template morph="${SUBJECTS_DIR}/${SUBJECT}/mri/transforms/${SUBJECT}_to_mni.m3z" # Example morph for vol in fa adc ivc; do vol_file="${OUTDIR}/${vol}-masked.mgz" outvol="${OUTDIR}/${vol}-masked_MNI.mgz" cmd=(mri_vol2vol --targ "$template" \ --m3z "$morph" \ --noDefM3zPath \ --reg "${OUTDIR}/register.dat" \ --mov "$vol_file" \ --o "$outvol" \ --interp "$interp" \ --no-save-reg) echo "${cmd[@]}" "${cmd[@]}" done Error: INFO: This REGISTER_DAT transform is valid only for volumes between COR types with c_(r,a,s) = 0. /mnt/data_analysis/freesurfer_data/sr_dti_analysis/subj02/subj02_fs/dtrecon/lowb.nii.gz /mnt/data_analysis/freesurfer_data/sr_dti_analysis/subj02/subj02_fs/mri/wmparc.mgz error: File exists error: LTAchangeType: src geometry must be valid Then I did the BB registration separately. bbregister --s subj02_fs \ --mov $DTI_DIR/lowb.nii.gz \ --dti \ --init-fsl \ --reg $DTI_DIR/register.dat Still, I am facing the same issue. Please provide some solutions. Best Ramesh

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Problem with applying FreeSurfer EasyAtlas warp format
by Chen, Yuqian 04 Dec '25

04 Dec '25

Dear FreeSurfer users, I’m attempting to use mri_warp_convert to convert an EasyAtlas transform into ITK format, but the resulting transform is incorrect when applied or visualized in 3D Slicer (see image below). The deformation field shrinks the brain, suggesting a possible scaling issue in the converted transform. Here is the command line I used: mri_warp_convert --inras sub-05_brain_warp.nii.gz --outitk sub-05_brain_warp-itk.nii.gz -g sub-05_brain.nii.gz<http://.nii.gz/> [Image] Has anyone encountered this behavior or knows whether additional steps are needed when converting EasyAtlas transforms to ITK format? Thank you for any guidance. Regards, Yuqian Chen, Ph.D. Postdoctoral Research Fellow, Harvard Medical School 399 Revolution Drive, Suite 1180, Somerville, MA 02145 ychen128(a)bwh.harvard.edu<mailto:ychen128@bwh.harvard.edu>

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Recon-all with Brainmask Input
by Anna Crawford 03 Dec '25

03 Dec '25

External Email - Use Caution Hello, I had a question about re-running recon-all with a precalculated brainmask. I have a brain mask that was created outside of FreeSurfer that I would like to use instead of the brainmask that is created in recon-all. I tried the following command (also with the mask in its original .nii form) and I get an error that the brainmask doesn't exist and thus does not continue throughout the pipeline (attached). recon-all -subjid test -i sub-HV3WJK_ses-MRI_rec-t1_N4norm.nii -xmask tweakedFSBrainMask2.mgz -all -noskullstrip error: mghRead(/home/acrawford/ATP_calibration_data/sub-HV3WJK/ses-MRI/run-001/fsNormPipeline_1/FStweakedMask/mri/brainmask.mgz, -1): could not open file\00 error: mri_em_register: could not open mask volume brainmask.mgz. \00 I have also tried running the full recon-all as is, then substituting in my brainmask and the skull-stripped T1 (brain.mgz) using the -autorecon2 -autorecon3 flags, but continue to run into errors. Additionally, I tried just using the skull-stripped T1 as the input file to recon-all -all which also did not work. Is there a way to run recon-all with an 'outside' mask? Thank you, Anna _________________________ Anna Crawford Senior Image Analyst Phone: +1 (475) 318-8228 https://secure-web.cisco.com/1xGC1sEawWmlv8GxcdUL2zP-fxq-1FmQXHLPVcKBZRMk30…<https://secure-web.cisco.com/1VLzeHvfaohhAFcoPLU3_Ow60GssgJipCmxB89BVY9HZda…> [cid:84668487-aed4-4dc5-8b0f-b61383239667] CONFIDENTIALITY NOTICE: Proprietary/Confidential Information belonging to XingImaging, LLC and its affiliates may be contained in this message. If you are not a recipient indicated or intended in this message (or responsible for delivery of this message to such person), or you think for any reason that this message may have been addressed to you in error, you may not use or copy or deliver this message to anyone else. In such case, you should destroy this message and are asked to notify the sender by reply e-mail.

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Freesurfer December 2025