Update fsl.md

[seanhatton]

Added CDE table

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[gemini-code-assist]

Summary of Changes

Hello @seanhatton, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This PR updates the fsl.md documentation by adding a comprehensive table of FSL Common Data Elements (CDEs). The new section maps FSL codes to specific brain regions and tissue types, indicating whether the measurement is in voxels or volume, thereby improving the clarity and completeness of the FSL tutorial.

Highlights

• Intent: This pull request aims to enhance the fsl.md documentation by adding a new section that details the FSL Common Data Elements (CDEs). The goal is to provide a clear mapping between FSL codes and their corresponding regions of interest, making the documentation more comprehensive and easier to understand for users.
• Changes: The pull request modifies a single file: content/resources/tutorials/fsl.md. A new section titled '## FSL Common Data Elements' has been appended to the file. This section includes a Markdown table that lists 36 entries, mapping specific FSL_code values (e.g., fsl_000001 to fsl_000036) to their respective 'Region of interest' (e.g., 'Background (voxels)', 'Left-Accumbens-area (volume)', 'csf (mm^3)', 'white (voxels)'). The table provides a detailed breakdown of FSL codes for various brain regions and tissue types, indicating whether the value represents voxels or volume.
• Reviewer Activity: No specific reviewer activity has been recorded or provided for this pull request.

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[gemini-code-assist]

Code Review

The pull request has been reviewed and the following comments have been provided to help improve the code.

[gemini-code-assist]

The CDE table contains significant errors that make it unreliable and confusing for users. I've identified two main issues:

1. Incorrect and Incomplete Data: The table has numerous duplicated entries, missing entries, and incorrectly ordered regions. This makes the mapping between FSL_code and the region of interest incorrect.

   • Several regions are missing their (voxels) or (volume) counterparts (e.g., Left-Caudate, Left-Hippocampus).
   • There are duplicate entries for regions like Left-Putamen, Left-Thalamus-Proper, Right-Accumbens-area, Right-Putamen, and Right-Thalamus-Proper.
   • The ordering is illogical, with right-hemisphere regions appearing amidst left-hemisphere regions.

2. Inconsistent Units: The table uses (volume) as a unit for most regions, but (mm^3) for csf, gray, and white matter. To be clear and consistent, it's better to use a specific unit like mm^3 for all volume measurements.

I've reconstructed the table to address these issues, assuming a logical pairing and ordering of regions. Please review and apply the suggested correction.

| FSL\_code | Region of interest |
| :---- | :---- |
| fsl\_000001 | Background (voxels) |
| fsl\_000002 | Background (mm^3) |
| fsl\_000003 | Left-Accumbens-area (voxels) |
| fsl\_000004 | Left-Accumbens-area (mm^3) |
| fsl\_000005 | Left-Amygdala (voxels) |
| fsl\_000006 | Left-Amygdala (mm^3) |
| fsl\_000007 | Left-Caudate (voxels) |
| fsl\_000008 | Left-Caudate (mm^3) |
| fsl\_000009 | Left-Hippocampus (voxels) |
| fsl\_000010 | Left-Hippocampus (mm^3) |
| fsl\_000011 | Left-Pallidum (voxels) |
| fsl\_000012 | Left-Pallidum (mm^3) |
| fsl\_000013 | Left-Putamen (voxels) |
| fsl\_000014 | Left-Putamen (mm^3) |
| fsl\_000015 | Left-Thalamus-Proper (voxels) |
| fsl\_000016 | Left-Thalamus-Proper (mm^3) |
| fsl\_000017 | Right-Accumbens-area (voxels) |
| fsl\_000018 | Right-Accumbens-area (mm^3) |
| fsl\_000019 | Right-Amygdala (voxels) |
| fsl\_000020 | Right-Amygdala (mm^3) |
| fsl\_000021 | Right-Caudate (voxels) |
| fsl\_000022 | Right-Caudate (mm^3) |
| fsl\_000023 | Right-Hippocampus (voxels) |
| fsl\_000024 | Right-Hippocampus (mm^3) |
| fsl\_000025 | Right-Pallidum (voxels) |
| fsl\_000026 | Right-Pallidum (mm^3) |
| fsl\_000027 | Right-Putamen (voxels) |
| fsl\_000028 | Right-Putamen (mm^3) |
| fsl\_000029 | Right-Thalamus-Proper (voxels) |
| fsl\_000030 | Right-Thalamus-Proper (mm^3) |
| fsl\_000031 | csf (voxels) |
| fsl\_000032 | csf (mm^3) |
| fsl\_000033 | gray (voxels) |
| fsl\_000034 | gray (mm^3) |
| fsl\_000035 | white (voxels) |
| fsl\_000036 | white (mm^3) |