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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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Re: Flatmap Coordinates Distance
by Glasser, Matthew 01 Dec '25

01 Dec '25

External Email - Use Caution We have tools in Connectome Workbench to compute geodesic distances accurately on the midthickness surface. If you have the same mesh topology between the flat map and a midthickness, you can just select the same vertices. Matt. From: "Fischl, Bruce R.,PHD" <BFISCHL(a)mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Monday, December 1, 2025 at 10:01 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Re: Flatmap Coordinates Distance Hi Tom Distances in the flat map should be in mm and within 10-15% of geodesics in the cortex. You could also use great circles on the sphere, which should give you about the same error percent, but you would need to scale the sphere so it has the same surface area as the cortex I believe Cheers Bruce From: Possidente, Thomas <tposside(a)bu.edu> Sent: Monday, December 1, 2025 9:53 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] Flatmap Coordinates Distance External Email - Use Caution Hi there, I have flattened a patch from fsaverage surface using mris_flatten and I would like to find the distance between two points on the flatmap. I believe that simply calculating the distance between coordinate points on the flatmap would not be interpretable because the units are no longer in millimeters (due to distortions during flattening). Please let me know if this is correct. I have found that I can map the vertex indices back into RAS 3D space and get the distance between 2 vertices that way, but because of cortical folding, it is different from the distance along the cortex between the two points. Is there any way to get the distance along the cortex between 2 vertices in interpretable units (ex. millimeters)? I am using Freesurfer 7.4.1 and Matlab 2023a to read in the any surface/patch/label files. Thank you for all the great work that you do! Best, Tom Thomas (Tom) Possidente | He/Him Doctoral Candidate | Boston University Brain, Behavior, & Cognition | Somers Lab ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Flatmap Coordinates Distance
by Possidente, Thomas 01 Dec '25

01 Dec '25

External Email - Use Caution Hi there, I have flattened a patch from fsaverage surface using mris_flatten and I would like to find the distance between two points on the flatmap. I believe that simply calculating the distance between coordinate points on the flatmap would not be interpretable because the units are no longer in millimeters (due to distortions during flattening). Please let me know if this is correct. I have found that I can map the vertex indices back into RAS 3D space and get the distance between 2 vertices that way, but because of cortical folding, it is different from the distance along the cortex between the two points. Is there any way to get the distance along the cortex between 2 vertices in interpretable units (ex. millimeters)? I am using Freesurfer 7.4.1 and Matlab 2023a to read in the any surface/patch/label files. Thank you for all the great work that you do! Best, Tom Thomas (Tom) Possidente | He/Him Doctoral Candidate | Boston University Brain, Behavior, & Cognition | Somers Lab

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Re: FreeSurfer License Key
by fsbuild 30 Nov '25

30 Nov '25

External Email - Use Caution  Please fill out the form at the URL listed below, and provide an email address where the license can be sent to you,https://secure-web.cisco.com/1oyFRTZrSHzcLBVKUWFPUQyoipUrNqfBLPB2s-4CDJ… On Nov 30, 2025, at 16:25, Batuhan Sönmez <batuhan.snmz5759(a)gmail.com> wrote:        External Email - Use Caution         _______________________________________________Freesurfer mailing list -- freesurfer(a)nmr.mgh.harvard.eduTo unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.edu/

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FreeSurfer License Key
by Batuhan Sönmez 30 Nov '25

30 Nov '25

External Email - Use Caution

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TumorSynth
by Cogno, Nicolo 26 Nov '25

26 Nov '25

Hi, I’ve just found out about TumorSynth on this webpage https://surfer.nmr.mgh.harvard.edu/fswiki/TumorSynth. I’ve installed FreeSurfer 8.1.0 and wanted to try it out, but the command doesn't exist. However, the webpage says that it should be available on FS v7.4.0 onwards. How should I proceed? I would like to try the multi-sequence input support. Thank you very much, Nicolò ------------------------------------------------------------------------------ Nicolò Cogno, Ph.D. Postdoctoral fellow in Radiation Oncology Massachusetts General Hospital / Harvard Medical School

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