hcp_fmri_stats

qx_utilities.hcp.hcp_fmri_stats.hcp_fmri_stats(sinfo, options, overwrite=False, thread=0)

hcp_fmri_stats [... processing options]

Runs the fMRI Statistics step of HCP Pipeline (fMRIStats.sh). Computes fMRI statistics including mTSNR, fCNR, and percent BOLD.

Warning

The code expects the input images to be named and present in the QuNex folder structure. The function will look into folder:

<session id>/hcp/<session id>

for data.

Parameters

--batchfile (str, default ''):

The batch.txt file with all the sessions information.

--sessionsfolder (str, default '.'):

The path to the study/sessions folder, where the imaging data is supposed to go.

--parsessions (int, default 1):

How many sessions to run in parallel.

--overwrite (str, default 'no'):

Whether to overwrite existing data (yes) or not (no).

--hcp_suffix (str, default ''):

Specifies a suffix to the session id if multiple variants are run, empty otherwise.

--logfolder (str, default ''):

The path to the folder where logs are to be stored, if other than default.

--log (str, default 'keep'):

Whether to keep ('keep') or remove ('remove') the temporary logs.

--hcp_concat_names (str, default 'fMRI_CONCAT_ALL'):

A comma separated list of fMRI concat names (e.g. tfMRI_ALLTASKS). If single-run FIX is used, this list must be exactly 1 element long.

--hcp_icafix_highpass (str, default '0'):

The high pass filter value used in ICA+FIX.

--hcp_fmristats_regname (str, default ''):

Surface registration name.

--hcp_fmristats_process_volume (str, default ''):

Whether to process volume data, TRUE or FALSE.

--hcp_fmristats_cleanup_effects (str, default ''):

Whether to compute cleanup effects metrics, TRUE or FALSE.

--hcp_fmristats_procstring (str, default ''):

Processing string suffix for cleaned data.

--hcp_fmristats_icamode (str, default ''):

ICA mode: 'sICA' for spatial ICA only, 'sICA+tICA' for combined spatial+temporal ICA.

--hcp_fmristats_fmri_names (str, default ''):

A comma separated list of fMRI single run names (only required if data was processed with single-run FIX, must be in order and complete).

--hcp_fmristats_tica_component_tcs (str, default ''):

Path to tICA timecourse CIFTI (required if tica_icamode is sICA+tICA).

--hcp_fmristats_tica_component_noise (str, default ''):

Path to tICA component noise indices text file (required if tica_icamode is sICA+tICA).

--hcp_matlab_mode (str, default default detailed below):

Specifies the Matlab version, can be 'interpreted', 'compiled' or 'octave'. Inside the container 'compiled' will be used, outside 'interpreted' is the default.

Output files

The results of this step will be generated and populated in the MNINonLinear folder inside the same session's root hcp folder.

Notes

hcp_fmri_stats parameter mapping:

QuNex parameter	HCPpipelines parameter
hcp_concat_names	concat-names
hcp_icafix_highpass	high-pass
hcp_fmristats_procstring	proc-string
hcp_fmristats_regname	reg-name
hcp_fmristats_process_volume	process-volume
hcp_fmristats_cleanup_effects	cleanup-effects
hcp_fmristats_icamode	ica-mode
hcp_fmristats_fmri_names	fmri-names
hcp_fmristats_tica_component_tcs	tica-component-tcs
hcp_fmristats_tica_component_noise	tica-component-noise
hcp_matlab_mode	matlab-run-mode

Examples

qunex hcp_fmri_stats \
    --batchfile=processing/batch.txt \
    --sessionsfolder=sessions \
    --hcp_concat_names="fMRI_CONCAT_ALL" \
    --hcp_icafix_highpass="2000" \
    --hcp_matlab_mode="interpreted"