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5.3 KiB
Markdown
123 lines
No EOL
5.3 KiB
Markdown
# Configuration Parameters for ALE
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This page provides a detailed explanation of the parameters available in the `config.yml` file. These settings control various aspects of the ALE analysis workflow. **Please note:** Many of these parameters are intended for advanced users. **DO NOT CHANGE THESE IF YOU ARE NOT AN ALE EXPERT!**
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---
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## Project Folder
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The **Project Folder** section specifies the file paths for key project documents:
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- **`analysis_info`**
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- **Default:** `"analysis_info.xlsx"`
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- **Description:** Excel file containing analysis-related information.
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- **`experiment_info`**
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- **Default:** `"experiment_info.xlsx"`
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- **Description:** Excel file containing details about the experiments.
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---
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## ALE Parameters
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These parameters control the main ALE analysis settings:
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- **`pool_experiments`**
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- **Default:** `True`
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- **Description:** When enabled, multiple experiments from the same paper are pooled into a single experiment. This helps in cases where individual experiments are not statistically independent.
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- **`tfce_enabled`**
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- **Default:** `True`
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- **Description:** Enables TFCE (Threshold-Free Cluster Enhancement) for multiple comparison correction. (See Frahm et al., 2022 for details.)
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- **`gm_masking`**
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- **Default:** `True`
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- **Description:** If enabled, the ALE map—and all subsequent maps—will be masked by the ICBM 10% GM mask to restrict the analysis to gray matter regions.
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- **`bin_steps`**
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- **Default:** `0.0001`
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- **Description:** Defines the size of the bins used in the Modeled Activation (MA) histogram. Smaller steps provide a finer resolution of the histogram.
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- **`cutoff_predict_enabled`**
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- **Default:** `True`
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- **Description:** When enabled, xgboost models are used to predict cutoff values instead of relying on monte carlo simulation. (Refer to Frahm et al., 2024.)
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- **`significance_threshold`**
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- **Default:** `0.05`
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- **Description:** The p-value required for significance. **Important:** This setting only applies if `cutoff_predict_enabled` is disabled.
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- **`cluster_forming_threshold`**
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- **Default:** `0.001`
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- **Description:** Sets the preliminary cluster forming threshold for cluster-level family-wise error correction. **Important:** This is only effective if `cutoff_predict_enabled` is disabled.
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- **`monte_carlo_iterations`**
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- **Default:** `5000`
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- **Description:** Number of iterations used for monte-carlo based multiple comparison correction. **Note:** Only applicable when `cutoff_predict_enabled` is disabled.
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- **`subsample_n`**
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- **Default:** `2500`
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- **Description:** The number of subsamples calculated for the probabilistic ALE algorithm.
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- **`contrast_permutations`**
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- **Default:** `10000`
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- **Description:** Specifies the number of iterations used in the classic contrast algorithm.
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- **`contrast_correction_method`**
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- **Default:** `"cFWE"`
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- **Options:** `"cFWE"`, `"vFWE"`, `"tfce"`
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- **Description:** Determines the correction method for the contrast algorithm.
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- `"cFWE"`: Cluster-level family-wise error correction (default).
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- `"vFWE"`: Voxel-level family-wise error correction.
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- `"tfce"`: Threshold-Free Cluster Enhancement correction.
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- **`difference_iterations`**
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- **Default:** `1000`
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- **Description:** Number of sub-iterations used in the balanced contrast algorithm.
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- **`nprocesses`**
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- **Default:** `2`
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- **Description:** Sets the number of parallel processes for various steps in the ALE algorithm. Adjust this number based on the capabilities of your machine.
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---
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## MA_Clustering Parameters
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These parameters control the settings for the Modeled Activation (MA) clustering process. **DO NOT CHANGE THESE IF YOU ARE NOT AN ALE EXPERT!**
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- **`max_clusters`**
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- **Default:** `10`
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- **Description:** The maximum number of clusters allowed in the analysis.
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- **`subsample_fraction`**
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- **Default:** `0.9`
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- **Description:** The fraction of data used in each subsampling iteration during the clustering process.
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- **`sampling_iterations`**
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- **Default:** `1000`
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- **Description:** Number of iterations for subsampling in the clustering algorithm.
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- **`null_iterations`**
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- **Default:** `5000`
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- **Description:** Number of iterations used to generate the null distribution for statistical testing.
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- **`correlation_type`**
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- **Default:** `"spearman"`
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- **Options:** `"spearman"`, `"pearson"`
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- **Description:** Specifies the type of correlation coefficient used to assess similarity between clusters.
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- **`clustering_method`**
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- **Default:** `"hierarchical"`
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- **Options:** `"hierarchical"`, `"kmeans"`
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- **Description:** Determines the clustering method. Hierarchical clustering is the default.
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- **`linkage_method`**
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- **Default:** `"complete"`
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- **Options:** `"complete"`, `"average"`, `"ward"`
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- **Description:** Defines the linkage method for hierarchical clustering.
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---
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## Important Notes
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- **Modifying Parameters:** Changes to the `config.yml` file can significantly affect the outcome of your analyses. Only adjust these parameters if you fully understand their implications.
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- **Further Reading:** For more detailed explanations and the latest updates, please refer to the ALE documentation and the cited publications (e.g., Frahm et al., 2022; Frahm et al., 2024). |