hcp_transmit_bias_individual#

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

hcp_transmit_bias_individual [... processing options]

Runs the HCP Transmit Bias Individual Only Pipeline.

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_gmwm_template (str, default ''):

Location of the GMWMtemplate, the file containing GM+WM volume ROI.

--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_group_corrected_myelin (str, default ''):

The group-corrected myelin file from AFI or B1Tx.

--hcp_afi_image (str, default ''):

Two-frame AFI image.

--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_b1tx_magnitude (str, default ''):

B1Tx magnitude image (for alignment).

--hcp_b1tx_phase (str, default ''):

B1Tx phase image.

--hcp_b1tx_phase_divisor (str, default '800'):

What to divide the phase map by to obtain proportion of intended

--hcp_pt_fmri_names (str, default <list of all BOLDs>):

A comma separated list of fMRI runs to use SE/SBRef files from. Set to a list of all BOLDs by default.

--hcp_pt_bbr_threshold (str, default '0.5'):

Mincost threshold for reinitializing fMRI bbregister with flirt (may need to be increased for aging-related reduction of gray/white contrast).

--hcp_myelin_template (str, default ''):

Expected transmit-corrected group-average myelin pattern (for testing correction parameters).

--hcp_group_uncorrected_myelin (str, default ''):

The group-average uncorrected myelin file (to set the appropriate scaling of the myelin template).

--hcp_pt_reference_value_file (str, default ''):

Text file containing the value in the pseudotransmit map where the flip angle best matches the intended angle, from the Phase2 group script.

--hcp_unproc_t1w_list (str, default ''):

A comma separated list of unprocessed T1w images, for correcting non-PSN data. You can set this to "auto" and QuNex will try to fill it automatically.

--hcp_unproc_t2w_list (str, default ''):

A comma separated list of unprocessed T2w images, for correcting non-PSN data. You can set this to "auto" and QuNex will try to fill it automatically.

--hcp_receive_bias_body_coil (str, default ''):

Image acquired with body coil receive, to be used with --hcp_receive_head_body_coil.

--hcp_receive_bias_head_coil (str, default ''):

Matched image acquired with head coil receive.

--hcp_raw_psn_t1w (str, default ''):

The bias-corrected version of the T1w image acquired with pre-scan normalize, which was used to generate the original myelin maps.

--hcp_raw_nopsn_t1w (str, default ''):

The uncorrected version of the --raw-psn-t1w image.

--hcp_transmit_res (str, default ''):

Resolution to use for transmit field, default equal to hcp_grayordinatesres.

--hcp_myelin_mapping_fwhm (str, default '5'):

The fwhm value to use in -myelin-style [5]

--hcp_old_myelin_mapping (flag, not set by default):

If myelin mapping was done using version 1.2.3 or earlier of wb_command, set this flag.

--hcp_gdcoeffs (str, default ''):

Path to a file containing gradient distortion coefficients.

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

The name of the registration used.

--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_gmwm_template

gmwm-template

hcp_regname

reg-name

hcp_transmit_mode

mode

hcp_group_corrected_myelin

group-corrected-myelin

hcp_afi_image

afi-image

hcp_afi_tr_one

afi-tr-one

hcp_afi_tr_two

afi-tr-two

hcp_afi_angle

afi-angle

hcp_b1tx_magnitude

b1tx-magnitude

hcp_b1tx_phase

b1tx-phase

hcp_b1tx_phase_divisor

b1tx-phase-divisor

hcp_pt_fmri_names

pt-fmri-names

hcp_pt_bbr_threshold

pt-bbr-threshold

hcp_myelin_template

myelin-template

hcp_group_uncorrected_myelin

group-uncorrected-myelin

hcp_pt_reference_value_file

pt-reference-value-file

hcp_unproc_t1w_list

unproc-t1w-list

hcp_unproc_t2w_list

unproc-t2w-list

hcp_receive_bias_body_coil

receive-bias-body-coil

hcp_receive_bias_head_coil

receive-bias-head-coil

hcp_raw_psn_t1w

raw-psn-t1w

hcp_raw_nopsn_t1w

raw-nopsn-t1w

hcp_transmit_res

transmit-res

hcp_myelin_mapping_fwhm

myelin-mapping-fwhm

hcp_old_myelin_mapping

old-myelin-mapping

hcp_gdcoeffs

scanner-grad-coeffs

hcp_regname

reg-name

hcp_lowresmesh

low-res-mesh

hcp_grayordinatesres

grayordinates-res

hcp_matlab_mode

matlab-run-mode

Examples

Example run:

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