Modifying init_vars - McIntosh-Lab/tvb-ukbb GitHub Wiki

You will likely need to modify some of the following variables in init_vars prior to running the pipeline. Some variables may or may not be present in init_vars depending on the branch.

FSLDIR - Installation directory for FSL. Do not change if you are using our Singularity image.

FSLGECUDAQ

QUEUE_STANDARD

QUEUE_MORE_MEM

QUEUE_MAX_MEM

SUBJECT_AGE_LIST - File path to a tab-separated values file (tsv), with each row containing a subject name (e.g. sub-102934) followed by their age in years.

AGE_SPECIFIC_TEMPLATE_LIST - File path to a tsv file, containing subject age deciles along with corresponding filenames for age-specific brain template images and fast prior images. Follow the format used here

SOFTDIR - Installation directory for tvb-pipeline. Do not change if you are using our Singularity image.

MCROOT - Installation directory for MATLAB. Do not change if you are using our Singularity image.

R_LIBS - Installation directory for R libraries. Do not change if you are using our Singularity image.

R_DIR - Installation directory for R. Do not change if you are using our Singularity image.

PARC_IMG - File path to parcellation image.

PARC_LUT - File path to parcellation look-up table. Must be a tsv file.

SUSCEPT_ROIS - File path to a masked image of signal dropout-susceptible ROIs.

TRAINING_FILE - FIX Training File.

SynB0 - Flag for toggling usage of Synb0-DisCo tool. Set to "y" to use SynB0.

PE_direction - Phase encoding direction.

topupValue - topup value. Set to a float (e.g. "0.1") to assign given topup value for all subjects processed by the pipeline or empty ("") to have the pipeline calculate topup values for each subject individually.

topupValue_default - Default topup value for a subject if the above topupValue variable is set to empty and topupValue calculations encounter an error. Set to a float (e.g. "0.1") to assign given topup value for subjects encountering a topupValue calculation error or empty ("") to error out such subjects.