Freesurfer March 2026

freesurfer@nmr.mgh.harvard.edu

29 participants
33 discussions

NextBrain segmentation tool not working
by Vittorio Rispoli 02 Mar '26

02 Mar '26

External Email - Use Caution Dear all, I unsuccessfully tried to run the NextBrain segmentation tool. Could you help me, please? My machine has freesurfer 8.0 installed - usually all look fine. After typing the command suggested in the nextbrain page, I have this error message vittorio@Disordini-Movimento-1 ~ % export FREESURFER_HOME=/Applications/freesurfer/8.0.0 source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer/8.0.0 FSFAST_HOME /Applications/freesurfer/8.0.0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/8.0.0/subjects MNI_DIR /Applications/freesurfer/8.0.0/mni vittorio@Disordini-Movimento-1 ~ % which mri_histo_atlas_segment_fireants /Applications/freesurfer/8.0.0/bin/mri_histo_atlas_segment_fireants vittorio@Disordini-Movimento-1 ~ % which mri_histo_atlas_segment_fireants /Applications/freesurfer/8.0.0/bin/mri_histo_atlas_segment_fireants vittorio@Disordini-Movimento-1 ~ % mri_histo_atlas_segment_fireants \ --i /Users/vittorio/Documents/Vittorio/prova_nextbrain/T1.nii.gz \ --o /Users/vittorio/Documents/Vittorio/prova_nextbrain/output_prova_nextbrain \ --device cpu \ --side left \ --mode invivo \ --threads 20 Incorrect number of arguments. Usage: mri_histo_atlas_segment_fireants INPUT_SCAN OUTPUT_DIRECTORY GPU THREADS [BF_MODE] Or, for help mri_histo_atlas_segment_fireants --help vittorio@Disordini-Movimento-1 ~ % --------------------------------------------------------- Do you have any suggestions to solve the issue? Best wishes Vittorio

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Freeview command line for "clear background" capability
by Jonathan Power 02 Mar '26

02 Mar '26

External Email - Use Caution In the Freeview 3.0 "Run Command" window, searching commands in the -h list, there are many ways to control image coloring. But I do not see anything for the "Clear background" capability. This capability is there in the GUI. If I load, say, a T1.mgz, and brainmask.mgz on top, for the brainmask.mgz volume, below the GUI color settings Color map / Window / Level / Min / Max sliders there are 3 buttons, the middle of which is "Clear background". Can this be switched on in a command line call? I ask because I would like to automate image generation where the within-mask tissue is normal grayscale, but the out-of-mask tissue is colored with a heat map, and this is nicely done when I can clear the brainmask background. Thanks, Jonathan

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Query on use of FreeSurfer with Clinical Epilepsy MRI Protocols (Anisotropic Voxel Size)
by Uttara Bakshi 02 Mar '26

02 Mar '26

External Email - Use Caution Dear FreeSurfer Support Team, Season's Greetings! I hope this email finds you well. May I take this opportunity to seek your support regarding the use of FreeSurfer for structural MRI data acquired using clinical epilepsy imaging protocols with non-isotropic voxel sizes in our hospital setting. To date, I have processed MRI data from over 90 epilepsy patients using *FreeSurfer v 6.0* (3T scanner 64-channel head coil, TA: 3:49 min; Voxel Size: 1.0 × 1.0 × 0.5 mm³; Acceleration factor: 2; Relative SNR: 1.00). The complete recon-all pipeline ran successfully for all subjects, generating cortical and subcortical segmentations as well as quantitative statistics files without any processing errors. However, I learnt that 1 mm³ isotropic resolution is recommended for optimal performance, although voxel sizes up to *1.3 × 1 × 1.3 mm³* are considered acceptable to reduce scan time or improve signal-to-noise ratio, as per FreeSurfer Wiki. Therefore recently, I have acquired one additional patient data using an isotropic protocol (1.0 × 1.0 × 1.0 mm³) and compared to epilepsy protocol mentioned above. To conclude , I got two different quantitative values. For example, in Left Hippocampus - Anisotropic : 3640.2 mm³ vs Isotropic : 3876.2 mm³ , Total intracranial volume- Anisotropic : 1504943.411530 mm³ vs Isotropic : 1529703.225834 mm3 , Mean cortical thickness – Anisotropic : 2.18512 mm vs Isotropic: 2.28844 mm. In this context, I would greatly appreciate your guidance on the following: 1. Would you recommend resampling 1 × 1 × 0.5 mm³ images to 1 mm³ isotropic resolution prior to running recon-all, or is it fine to process the native anisotropic resolution data? 2. Are there any appropriate FreeSurfer steps or commands to convert my already acquired 1 × 1 × 0.5 mm³ MRI data to isotropic resolution before running the FreeSurfer recon-all pipeline? 3. Are there any known limitations, biases, or segmentation inaccuracies, particularly affecting hippocampal volumetry or cortical thickness estimates, when FreeSurfer is applied to anisotropic voxel data in epilepsy research like I did? I am attaching the recon-all log files of both the protocols here. Thank you very much for your time and guidance. I would greatly appreciate your recommendations. -- Warm regards, *Uttara Bakshi* *Doctoral Fellow* *Institute Of Neurosciences Kolkata, India.*

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Freesurfer March 2026