Importing Freesurfer Brain Segmentation into Brainsuite

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    • #3896

      If I have already done the brain segmentation and cortical surface extractions in Freesurfer can I import those into brainsuite and then just run the label and register a brain part of the pipeline to save time?

    • #4931

    • #5012

      Certainly! To import FreeSurfer brain segmentation into BrainSuite, follow these simple steps:

      1. Convert FreeSurfer files to NIfTI format: Use the mri_convert command to convert .mgz files (like brain. mgz and aparc+aseg.mgz) to .nii or .nii.gz format.


      mri_convert brain.nii.gz

      mri_convert aparc+aseg.mgz aparc+aseg.nii.gz

      2. Open BrainSuite: Start BrainSuite and use the ‘Open Volume’ option to load the .nii files you just converted.

      3. Load Surface Files: Convert FreeSurfer surface files (e.g., lh. pial, rh. pial) to a format (like .ply) that can be read in BrainSuite. Use mris_convert for this purpose.

      4. Visualize and Analyze: With your files now in BrainSuite, you can visualize and analyze the data using BrainSuite’s tools.

      This streamlined process will help you leverage BrainSuite’s powerful features for your neuroimaging analysis.

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