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42 changes: 42 additions & 0 deletions content/resources/tutorials/fsl.md
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Original file line number Diff line number Diff line change
Expand Up @@ -65,3 +65,45 @@ e.g.
fslsegstats2nidm -add_de -d ./proj/derivatives/fsl/sub-01/segstats.json -subjid sub-01 -n ./proj/nidm.ttl
```
The FSL annotations will append to the nidm.ttl so all the project data can be queried in a central file.

## FSL Common Data Elements
Here is the mapping between FSL CDEs and regions of interest.

| FSL\_code | Region of interest |
| :---- | :---- |
| fsl\_000001 | Background (voxels) |
| fsl\_000002 | Background (volume) |
| fsl\_000003 | Left-Accumbens-area (voxels) |
| fsl\_000004 | Left-Accumbens-area (volume) |
| fsl\_000005 | Left-Amygdala (voxels) |
| fsl\_000006 | Left-Amygdala (volume) |
| fsl\_000007 | Left-Caudate (voxels) |
| fsl\_000008 | Left-Hippocampus (volume) |
| fsl\_000009 | Left-Pallidum (voxels) |
| fsl\_000010 | Left-Putamen (volume) |
| fsl\_000011 | Left-Thalamus-Proper (voxels) |
| fsl\_000012 | Right-Accumbens-area (volume) |
| fsl\_000013 | Left-Putamen (voxels) |
| fsl\_000014 | Left-Putamen (volume) |
| fsl\_000015 | Left-Thalamus-Proper (voxels) |
| fsl\_000016 | Left-Thalamus-Proper (volume) |
| fsl\_000017 | Right-Accumbens-area (voxels) |
| fsl\_000018 | Right-Accumbens-area (volume) |
| fsl\_000019 | Right-Amygdala (voxels) |
| fsl\_000020 | Right-Amygdala (volume) |
| fsl\_000021 | Right-Caudate (voxels) |
| fsl\_000022 | Right-Hippocampus (volume) |
| fsl\_000023 | Right-Pallidum (voxels) |
| fsl\_000024 | Right-Putamen (volume) |
| fsl\_000025 | Right-Thalamus-Proper (voxels) |
| fsl\_000026 | Right-Accumbens-area (volume) |
| fsl\_000027 | Right-Putamen (voxels) |
| fsl\_000028 | Right-Putamen (volume) |
| fsl\_000029 | Right-Thalamus-Proper (voxels) |
| fsl\_000030 | Right-Thalamus-Proper (volume) |
| 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) |
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critical

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) |

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