hcp_task_fmri_analysis#

qx_utilities.hcp.process_hcp.hcp_task_fmri_analysis(sinfo, options, overwrite=False, thread=0)#

hcp_task_fmri_analysis [... processing options]

Runs the Diffusion step of HCP Pipeline (TaskfMRIAnalysis.sh).

Warning

The requirement for this command is a successful completion of the minimal HCP preprocessing pipeline.

Parameters

--batchfile (str, default ''):

The batch.txt file with all the session's 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.

--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 runlogs and comlogs are to be stored, if other than default.

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

Whether to keep ('keep') or remove ('remove') the temporary logs once jobs are completed. When a comma or pipe ('|') separated list is given, the log will be created at the first provided location and then linked or copied to other locations. The valid locations are:

'study' (for the default: <study>/processing/logs/comlogs location)
'session' (for <sessionid>/logs/comlogs)
'hcp' (for <hcp_folder>/logs/comlogs)
'<path>' (for an arbitrary directory).

--hcp_task_lvl1tasks (str, default ''):

List of task fMRI scan names, which are the prefixes of the time series filename for the TaskName task. Multiple task fMRI scan names should be provided as a comma separated list.

--hcp_task_lvl1fsfs (str, default ''):

List of design names, which are the prefixes of the fsf filenames for each scan run. Should contain same number of design files as time series images in --hcp_task_lvl1tasks option (N-th design will be used for N-th time series image). Provide a comma separated list of design names. If no value is passed to --hcp_task_lvl1fsfs, the value will be set to --hcp_task_lvl1tasks.

--hcp_task_lvl2task (str, default NONE):

Name of Level2 subdirectory in which all Level2 feat directories are written for TaskName.

--hcp_task_lvl2fsf (str, default ''):

Prefix of design.fsf filename for the Level2 analysis for TaskName. If no value is passed to --hcp_task_lvl2fsf, the value will be set to the same list passed to --hcp_task_lvl2task.

--hcp_task_summaryname (str, default 'NONE'):

Naming convention for single-subject summary directory. Mandatory when running Level1 analysis only, and should match naming of Level2 summary directories. Default when running Level2 analysis is derived from --hcp_task_lvl2task and --hcp_task_lvl2fsf options 'tfMRI_TaskName/DesignName_TaskName'.

--hcp_task_confound (str, default 'NONE'):

Confound matrix text filename (e.g., output of fsl_motion_outliers). Assumes file is in <SubjectID>/MNINonLinear/Results/<ScanName>.

--hcp_bold_smoothFWHM (int, default 2):

Smoothing FWHM that matches what was used in the fMRISurface pipeline.

--hcp_bold_final_smoothFWHM (int, default 2):

Value (in mm FWHM) of total desired smoothing, reached by calculating the additional smoothing required and applying that additional amount to data previously smoothed in fMRISurface. Default=2, which is no additional smoothing above HCP minimal preprocessing pipelines outputs.

--hcp_task_highpass (int, default 200):

Apply additional highpass filter (in seconds) to time series and task design. This is above and beyond temporal filter applied during preprocessing. To apply no additional filtering, set to 'NONE'.

--hcp_task_lowpass (str, default 'NONE'):

Apply additional lowpass filter (in seconds) to time series and task design. This is above and beyond temporal filter applied during preprocessing. Low pass filter is generally not advised for Task fMRI analyses.

--hcp_task_procstring (str, default 'NONE'):

String value in filename of time series image, specifying the additional processing that was previously applied (e.g., FIX-cleaned data with 'hp2000_clean' in filename).

--hcp_regname (str, default 'MSMSulc'):

Name of surface registration technique.

--hcp_grayordinatesres (int, default 2):

Value (in mm) that matches value in 'Atlas_ROIs' filename.

--hcp_lowresmesh (int, default 32):

Value (in mm) that matches surface resolution for fMRI data.

--hcp_task_vba (flag, optional):

A flag for using VBA. Only use this flag if you want unconstrained volumetric blurring of your data, otherwise set to NO for faster, less biased, and more senstive processing (grayordinates results do not use unconstrained volumetric blurring and are always produced). This flag is not set by defult.

--hcp_task_parcellation (str, default 'NONE'):

Name of parcellation scheme to conduct parcellated analysis. Default setting is NONE, which will perform dense analysis instead. Non-greyordinates parcellations are not supported because they are not valid for cerebral cortex. Parcellation supersedes smoothing (i.e. no smoothing is done).

--hcp_task_parcellation_file (str, default 'NONE'):

Absolute path to the parcellation dlabel file.

Output files

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

Notes

Mapping of QuNex parameters onto HCP Pipelines parameters:

Below is a detailed specification about how QuNex parameters are mapped onto the HCP Pipelines parameters.

QuNex parameter	HCPpipelines parameter
`hcp_task_lvl1task`	`lvl1tasks`
`hcp_task_lvl1fsfs`	`lvl1fsfs`
`hcp_task_lvl2task`	`lvl2task`
`hcp_task_lvl2fsf`	`lvl2fsf`
`hcp_task_confound`	`confound`
`hcp_bold_smoothFWHM`	`origsmoothingFWHM`
`hcp_bold_final_smoothFWHM`	`finalsmoothingFWHM`
`hcp_task_highpass`	`highpassfilter`
`hcp_task_lowpass`	`lowpassfilter`
`hcp_task_procstring`	`procstring`
`hcp_regname`	`regname`
`hcp_grayordinatesres`	`grayordinatesres`
`hcp_lowresmesh`	`lowresmesh`
`hcp_task_vba`	`vba`
`hcp_task_parcellation`	`parcellation`
`hcp_task_parcellation_file`	`parcellationfile`

Examples

First level HCP TaskfMRIanalysis:

qunex hcp_task_fmri_analysis \
    --sessionsfolder="<study_path>/sessions" \
    --batchfile="<study_path>/processing/batch.txt" \
    --hcp_task_lvl1tasks="tfMRI_GUESSING_PA" \
    --hcp_task_summaryname="tfMRI_GUESSING/tfMRI_GUESSING"

Second level HCP TaskfMRIanalysis:

qunex hcp_task_fmri_analysis \
    --sessionsfolder="<study_path>/sessions" \
    --batchfile="<study_path>/processing/batch.txt" \
    --hcp_task_lvl1tasks="tfMRI_GUESSING_AP@tfMRI_GUESSING_PA" \
    --hcp_task_lvl2task="tfMRI_GUESSING"

QuNex documentation

hcp_task_fmri_analysis

hcp_task_fmri_analysis#