# HCP ICAFix pipeline

````{admonition} Prerequisites
* [HCP fMRISurface](../UsageDocs/HCPfMRISurface)
````

For all HCP pipeline steps please refer to [Running the HCP pipeline](../UsageDocs/RunningPreprocessHCP). For an overview on how to prepare data and run the HCP preprocessing steps, see [Overview of steps for running the HCP pipeline](../UsageDocs/HCPPreprocessing).

The ICAFix implementation in the QuNex suite covers all steps from the HCP ICAFix pipeline. To achieve this, three commands are implemented:

* [`hcp_icafix`](../../api/gmri/hcp_icafix.rst)

    Runs the ICAFix step of HCP Pipelines. This step attempts to auto-classify ICA components into good and bad, so that the bad components can be then removed from the 4D fMRI data. If ICAFix step finishes successfully PostFix step will be ran automatically, to disable this set the `--hcp_icafix_postfix` to `FALSE`.

* [`hcp_post_fix`](../../api/gmri/hcp_post_fix.rst)

    Runs the PostFix step of HCP Pipelines. This step creates Workbench scene files that can be used to visually review the signal vs. noise classification generated by ICAFix.

* [`hcp_reapply_fix`](../../api/gmri/hcp_reapply_fix.rst)

    Runs the ReApplyFix step of HCP Pipelines. This function executes two steps, first it applies the hand reclassifications of noise and signal components from FIX using the ReclassifyAsNoise.txt and ReclassifyAsSignal.txt input files. Next it executes the HCP Pipeline's ReApplyFix or ReApplyFixMulti.

If the `--hcp_icafix_bolds` parameter is not provided ICAFix will bundle all bolds together and execute multi-run HCP ICAFix. The concatenated file will be named `fMRI_CONCAT_ALL`.

````{warning}
If session has many bolds such processing requires a lot of computational resources.
````

Instead of full bold names, you can also use bold tags from the batch file. Assume that the text bellow is an excerpt from a `batch.txt` file:

``` bash
1: bold1:REST1         : rfMRI_REST1_PA ...
2: bold2:REST1         : rfMRI_REST1_AP ...
3: bold1:REST2         : rfMRI_REST2_PA ...
4: bold2:REST2         : rfMRI_REST2_AP ...
5: bold4:GUESSING      : tfMRI_GUESSING_PA ...
6: bold5:GUESSING      : tfMRI_GUESSING_AP ...
```

Using this batch file one might set `--hcp_icafix_bolds=REST1` to execute a single-run HCP ICAFix on `rfMRI_REST1_PA` and `rfMRI_REST1_AP` or `hcp_icafix_bolds=CONCAT_REST2:REST2|CONCAT_GUESSING:GUESSING` to execute two multi-runs of HCP ICAFix, one on bolds tagged with `REST2` (`rfMRI_REST2_PA`, `rfMRI_REST2_AP`) and the other on bolds tagged with `GUESSING` (`tfMRI_GUESSING_PA`, `tfMRI_GUESSING_AP`).

The full list of command's parameters along with example calls can be found at:

* [`hcp_icafix`](../../api/gmri/hcp_icafix)
* [`hcp_post_fix`](../../api/gmri/hcp_post_fix)
* [`hcp_reapply_fix`](../../api/gmri/hcp_reapply_fix)