hcp_transmit_bias_group_average_corrected_maps

qx_utilities.hcp.hcp_transmit_bias_group_average_corrected_maps.hcp_transmit_bias_group_average_corrected_maps(sessions, options, overwrite=True, thread=0)

hcp_transmit_bias_group_average_corrected_maps [... processing options]

Runs the HCP Transmit Bias Pipeline Phase 4, Group Average Corrected Maps.

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). Note that previous data is deleted before the run, so in the case of a failed command run, previous results are lost.

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

Input registration name.

--hcp_transmit_mode (str, default ''):

What type of transmit bias correction to apply, options and required inputs are:

a) AFI: actual flip angle sequence with two different echo times, requires the following parameters: afi-tr-one,afi-tr-two, afi-angle, transmit-group-name.

b) B1Tx: b1 transmit sequence magnitude/phase pair, requires the following parameters: transmit-group-name.

c) PseudoTransmit: use spin echo fieldmaps, SBRef, and a template transmit-corrected myelin map to derive empirical correction, requires the following parameters: average-myelin, group-average-name, voltages

--hcp_transmit_group_name (str, default ''):

Name for the subgroup of subjects that have good AFI or B1Tx data (e.g. Partial)

--hcp_average_myelin (str, default ''):

CIFTI file of group average uncorrected myelin.

--hcp_outgroupname (str, default ''):

Output folder inside studyfolder

--hcp_voltages (str, default ''):

Text file of scanner calibrated transmit voltages for each subject. If the file does not exist, QuNex will attempt to create it by extracting TxrefAmp from each session's JSON metadata file.

--hcp_afi_tr_one (str, default ''):

TR of first AFI frame.

--hcp_afi_tr_two (str, default ''):

TR of second AFI frame.

--hcp_afi_angle (str, default ''):

Target flip angle of AFI sequence.

--hcp_lowresmesh (int, default 32):

Mesh resolution.

--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.

Notes

hcp_transmit_bias_group_average_corrected_maps parameter mapping:

QuNex parameter	HCPpipelines parameter
sessionsfolder	study-folder
sessions / session list	subject-list
hcp_regname	reg-name
hcp_transmit_mode	mode
hcp_outgroupname	group-average-name
hcp_transmit_group_name	transmit-group-name
hcp_voltages	voltages
hcp_afi_tr_one	afi-tr-one
hcp_afi_tr_two	afi-tr-two
hcp_afi_angle	afi-angle
hcp_average_myelin	average-myelin
hcp_lowresmesh	low-res-mesh
hcp_matlab_mode	matlab-run-mode

Examples

Example run:

qunex hcp_transmit_bias_group_average_corrected_maps \
    --sessionsfolder="<path_to_study_folder>/sessions" \
    --batchfile="<path_to_study_folder>/processing/batch.txt"