hcp_transmit_bias_group_average_fit

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

hcp_transmit_bias_group_average_fit [... processing options]

Runs the HCP Transmit Bias Pipeline Phase 2, Group Average Fit.

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-image, afi-tr-one,afi-tr-two, afi-angle, group-corrected-myelin.

b) B1Tx: b1 transmit sequence magnitude/phase pair, requires the following parameters: b1tx-magnitude, b1tx-phase, group-corrected-myelin.

c) PseudoTransmit: use spin echo fieldmaps, SBRef, and a template transmit-corrected myelin map to derive empirical correction, requires the following parameters: pt-fmri-names, myelin-template, group-uncorrected-myelin, reference-value.

--hcp_transmit_group_name (str, default ''):

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

--hcp_outgroupname (str, default ''):

Output folder inside studyfolder

--hcp_gmwm_template (str, default ''):

Output file for GM+WM volume ROI

--hcp_group_uncorrected_myelin (str, default ''):

Output cifti file for group average of uncorrected myelin

--hcp_all_uncorrected_myelin (str, default ''):

Output cifti file for concatenated uncorrected myelin

--hcp_manual_receive (str, default 'false'):

Whether Phase1 used unprocessed scans to correct for not using PSN when acquiring scans, default false

--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_pt_reference_value_file (str, default ''):

output text file for PseudoTransmit reference value.

--hcp_lowresmesh (int, default 32):

Mesh resolution.

--hcp_grayordinatesres (int, default 2):

The size of voxels for the subcortical and cerebellar data in grayordinate space in mm.

--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_individual parameter mapping:

QuNex parameter	HCPpipelines parameter
hcp_regname	reg-name
hcp_transmit_mode	mode
hcp_outgroupname	group-average-name
hcp_gmwm_template	gmwm-template-out
hcp_group_uncorrected_myelin	average-myelin-out
hcp_all_uncorrected_myelin	all-myelin-out
hcp_manual_receive	manual-receive
hcp_transmit_group_name	transmit-group-name
hcp_afi_tr_one	afi-tr-one
hcp_afi_tr_two	afi-tr-two
hcp_afi_angle	afi-angle
hcp_pt_reference_value_file	reference-value-out
hcp_lowresmesh	low-res-mesh
hcp_grayordinatesres	grayordinates-res
hcp_matlab_mode	matlab-run-mode

Examples

Example run:

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