hcp_apply_auto_reclean

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

hcp_apply_auto_reclean [... processing options]

Runs the ApplyAutoRecleanPipeline step of HCP Pipeline (ApplyAutoRecleanPipeline.sh).

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 files:

MNINonLinear/Results/<boldname>/<boldname>.nii.gz

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.

--parelements (int, default 1):

How many elements (e.g.bolds) 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.

--hcp_icafix_bolds (str, default ''):

Specify a list of bolds for ICAFix. If a multi run ICAFix was ran you need to specifty the group/concatenation name along with a list of bolds, e.g. "<group1>:<boldname1>,<boldname2>|<group2>:<boldname3>,<boldname4>". In the case of a single run, you need to specify a comma separated list of bolds, e.g. "<boldname1>,<boldname2>". If this parameter is not provided the command will use the same default as hcp_icafix, it will bundle all bolds together with the concatenated file named fMRI_CONCAT_ALL.

--hcp_icafix_highpass (int, default 0):

Value for the highpass filter, [0] for multi-run HCP ICAFix and [2000] for single-run HCP ICAFix.

--hcp_bold_res (str, default '2'):

Resolution of data.

--hcp_autoreclean_timepoints (str, default ''):

Output spectra size for sICA individual projection, RunsXNumTimePoints, like '4800'.

--hcp_lowresmesh (int, default 32):

Mesh resolution.

--hcp_autoreclean_model_folder (str, default '<$HCPPIPEDIR/ICAFIX/rclean_models>'):

The folder path of the trained models. Will use the HCP's model folder by default.

--hcp_autoreclean_model_to_use (str, default 'MLP,RandomForest'):

A comma separeted list of models to use. HCP available models are: MLP, RandomForest, Xgboost and XgboostEnsemble. Will use MLP and RandomForest by default.

--hcp_autoreclean_vote_threshold (int):

A decision threshold for determing reclassifications, should be less than to equal to the number of models to use.

--hcp_matlab_mode (str, default 'compiled'):

The matlab run mode, can be 'compiled', 'interpreted' or 'octave'. Default is 'compiled'.

Output files

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

Notes

hcp_apply_auto_reclean parameter mapping:

QuNex parameter	HCPpipelines parameter
hcp_icafix_bolds	fmri-names
hcp_icafix_bolds	mrfix-concat-name
hcp_icafix_highpass	bandpass
hcp_bold_res	fmri-resolution
hcp_autoreclean_timepoints	subject-expected-timepoints
hcp_lowresmesh	low-res-mesh
hcp_autoreclean_model_folder	model-folder
hcp_autoreclean_model_to_use	model-to-use
hcp_autoreclean_vote_threshold	vote-threshold
hcp_matlab_mode	matlabrunmode

Examples

qunex hcp_apply_auto_reclean \
    --batchfile=processing/batch.txt \
    --sessionsfolder=sessions \
    --hcp_autoreclean_timepoints="4800"

qunex hcp_apply_auto_reclean \
    --batchfile=processing/batch.txt \
    --sessionsfolder=sessions \
    --hcp_icafix_bolds="GROUP_1:BOLD_1,BOLD_2|GROUP_2:BOLD_3,BOLD_4" \
    --hcp_autoreclean_timepoints="4800" \
    --hcp_matlab_mode="interpreted"