Brain MRI Volumetry Research
Budget: $2 – $8 USD
I am running a research study that tracks structural changes in the brain, and I need precise volumetric measurements for gray matter, white matter, and cerebrospinal fluid on a series of MRI scans. The images are already acquired (high-resolution T1-weighted, NIfTI format) and stored on a secure server; I will give you SSH or cloud access once we start.
Your task is to run a robust segmentation pipeline—FreeSurfer, FSL FAST, SPM CAT, or an equivalent tool you are comfortable with—and deliver clean, reproducible volume estimates. While automation is welcome, any obvious mis-segmentations must be manually corrected so the final numbers are publication-ready.
Deliverables
• A CSV or Excel sheet listing total and, if available, regional GM, WM, and CSF volumes for every subject
• The corresponding segmentation masks (NIfTI) so I can verify or reuse them
• A brief “methods” note outlining the exact software versions, parameters, and QC steps you applied
Acceptance criteria
• GM, WM, and CSF volumes for each scan differ by no more than ±3 % from a FreeSurfer baseline I will provide for a test case
• No visible skull, dura, or blood vessels remain in the GM mask when overlaid on the original image
• All deliverables pass a random visual spot-check on three subjects
If you have recent experience publishing brain volumetry data or have sample reports to share, let me know when you bid so I can see your workflow in action.
Your task is to run a robust segmentation pipeline—FreeSurfer, FSL FAST, SPM CAT, or an equivalent tool you are comfortable with—and deliver clean, reproducible volume estimates. While automation is welcome, any obvious mis-segmentations must be manually corrected so the final numbers are publication-ready.
Deliverables
• A CSV or Excel sheet listing total and, if available, regional GM, WM, and CSF volumes for every subject
• The corresponding segmentation masks (NIfTI) so I can verify or reuse them
• A brief “methods” note outlining the exact software versions, parameters, and QC steps you applied
Acceptance criteria
• GM, WM, and CSF volumes for each scan differ by no more than ±3 % from a FreeSurfer baseline I will provide for a test case
• No visible skull, dura, or blood vessels remain in the GM mask when overlaid on the original image
• All deliverables pass a random visual spot-check on three subjects
If you have recent experience publishing brain volumetry data or have sample reports to share, let me know when you bid so I can see your workflow in action.