HCP MSMAll pipeline#


For all HCP pipeline steps please refer to Running the HCP pipeline. For an overview on how to prepare data and run the HCP preprocessing steps, see Overview of steps for running the HCP pipeline.

The integration of HCP MSMAll pipelines into the QuNex suite implements two commands:

  • hcp_msmall

    Runs the MSMAll step of HCP Pipelines. This step computes the MSMAll registration based on resting-state connectivity, resting-state topography, and myelin-map architecture.

  • hcp_dedrift_and_resample

    Runs the DeDriftAndResample step of HCP Pipelines. This step applies the MSMAll registration to a specified set of maps and fMRI runs.

Note that if the MSMAll step finishes successfully, the DeDriftAndResample step will execute automatically. To disable this automatic execution of DeDriftAndResample set the --hcp_msmall_resample parameter to FALSE.

MSMAll/DeDriftAndResample is intended for use with fMRI runs cleaned with hcp_icafix. Except for specialized/expert-user situations, the --hcp_icafix_bolds parameter should be identical to what was used in hcp_icafix. If hcp_icafix_bolds is not provided MSMAll/DeDriftAndResample will assume multi-run ICAFix was executed with all bolds bundled together in a single concatenation called fMRI_CONCAT_ALL. (This is the default behavior if hcp_icafix_bolds parameter is not provided in the case of hcp_icafix).

A key parameter in hcp_msmall is hcp_msmall_bolds, which controls the fMRI runs that enter into the computation of the MSMAll registration. Since MSMAll registration was designed to be computed from resting-state scans, this should be a list of the resting-state fMRI scans that you want to contribute to the computation of the MSMAll registration.

However, it is perfectly fine to apply the MSMAll registration to task fMRI scans in the DeDriftAndResample step. The fMRI scans to which the MSMAll registration is applied are controlled by the --hcp_icafix_bolds parameter, since typically one wants to apply the MSMAll registration to the same full set of fMRI scans that were cleaned using hcp_icafix.

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

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_msmall_bolds=REST1,REST2 to conveniently specify all REST bolds for the --hcp_msmall_bolds parameter.

Specific parameters#

Besides the shared parameters for HCP functions mentioned in the General settings and information on HCP preprocessing pipeline Wiki hcp_msmall and hcp_dedrift_and_resample use specific parameters that are listed in their online command reference.