(base) brainmappers@brainmappers-desktop5:/media/myelin/Yash/refactoredHCPI-Code/OldFunctions$ source /media/myelin/Yash/refactoredHCPI-Code/SetUpHCPPipeline.sh (base) brainmappers@brainmappers-desktop5:/media/myelin/Yash/refactoredHCPI-Code/OldFunctions$ ./PreFreeSurferPipeline_old.sh --help PreFreeSurferPipeline_old.sh Usage: PreFreeSurferPipeline_old.sh [options] --path= Path to study data folder (required) Used with --subject input to create full path to root directory for all outputs generated as path/subject --subject= Subject ID (required) Used with --path input to create full path to root directory for all outputs generated as path/subject --t1= An @ symbol separated list of full paths to T1-weighted (T1w) structural images for the subject (required) --t2= An @ symbol separated list of full paths to T2-weighted (T2w) structural images for the subject (required for hcp-style data, can be NONE for legacy-style data, see --processing-mode option) --t1template= MNI T1w template --t1templatebrain= Brain extracted MNI T1wTemplate --t1template2mm= MNI 2mm T1wTemplate --t2template= MNI T2w template --t2templatebrain= Brain extracted MNI T2wTemplate --t2template2mm= MNI 2mm T2wTemplate --templatemask= Brain mask MNI Template --template2mmmask= Brain mask MNI 2mm Template --brainsize= Brain size estimate in mm, 150 for humans --fnirtconfig= FNIRT 2mm T1w Configuration file --fmapmag= Siemens/Philips Gradient Echo Fieldmap magnitude file --fmapphase= Siemens/Philips Gradient Echo Fieldmap phase file --fmapgeneralelectric= General Electric Gradient Echo Field Map file Two volumes in one file 1. field map in deg 2. magnitude --echodiff= Delta TE in ms for field map or "NONE" if not used --SEPhaseNeg={, NONE} For spin echo field map, path to volume with a negative phase encoding direction (LR in HCP data), set to "NONE" if not using Spin Echo Field Maps --SEPhasePos={, NONE} For spin echo field map, path to volume with a positive phase encoding direction (RL in HCP data), set to "NONE" if not using Spin Echo Field Maps --seechospacing= Effective Echo Spacing of Spin Echo Field Map, (in seconds) or "NONE" if not used --seunwarpdir={x,y,NONE} Phase encoding direction (according to the *voxel* axes) or={i,j,NONE} of the spin echo field map. (Only applies when using a spin echo field map.) --t1samplespacing= T1 image sample spacing, "NONE" if not used --t2samplespacing= T2 image sample spacing, "NONE" if not used --unwarpdir={x,y,z,x-,y-,z-} Readout direction of the T1w and T2w images (according to the *voxel axes) or={i,j,k,i-,j-,k-} (Used with either a gradient echo field map or a spin echo field map) --gdcoeffs= File containing gradient distortion coefficients, Set to "NONE" to turn off --avgrdcmethod= Averaging and readout distortion correction method. See below for supported values. "NONE" average any repeats with no readout distortion correction "TOPUP" average any repeats and use Spin Echo Field Maps for readout distortion correction "PhilipsFieldMap" average any repeats and use Philips specific Gradient Echo Field Maps for readout distortion correction "GeneralElectricFieldMap" average any repeats and use General Electric specific Gradient Echo Field Maps for readout distortion correction "SiemensFieldMap" average any repeats and use Siemens specific Gradient Echo Field Maps for readout distortion correction "FIELDMAP" equivalent to "SiemensFieldMap" (preferred) This option value is maintained for backward compatibility. --topupconfig= Configuration file for topup or "NONE" if not used [--bfsigma=] Bias Field Smoothing Sigma (optional) [--custombrain=(NONE|MASK|CUSTOM)] If PreFreeSurfer has been run before and you have created a custom brain mask saved as "/T1w/custom_acpc_dc_restore_mask.nii.gz", specify "MASK". If PreFreeSurfer has been run before and you have created custom structural images, e.g.: - "/T1w/T1w_acpc_dc_restore_brain.nii.gz" - "/T1w/T1w_acpc_dc_restore.nii.gz" - "/T1w/T2w_acpc_dc_restore_brain.nii.gz" - "/T1w/T2w_acpc_dc_restore.nii.gz" to be used when peforming MNI152 Atlas registration, specify "CUSTOM". When "MASK" or "CUSTOM" is specified, only the AtlasRegistration step is run. If the parameter is omitted or set to NONE (the default), standard image processing will take place. If using "MASK" or "CUSTOM", the data still needs to be staged properly by running FreeSurfer and PostFreeSurfer afterwards. NOTE: This option allows manual correction of brain images in cases when they were not successfully processed and/or masked by the regular use of the pipelines. Before using this option, first ensure that the pipeline arguments used were correct and that templates are a good match to the data. [--processing-mode=(HCPStyleData| Controls whether the HCP acquisition and processing guidelines should be treated as requirements. LegacyStyleData)] "HCPStyleData" (the default) follows the processing steps described in Glasser et al. (2013) and requires 'HCP-Style' data acquistion. "LegacyStyleData" allows additional processing functionality and use of some acquisitions that do not conform to 'HCP-Style' expectations. In this script, it allows not having a high-resolution T2w image.