Processing check files#

When running HCPpipeline preprocessing, the user can request that the success of processing is verified by checking for presence of all files that should be generated by the specific pipeline. This request is specified by hcp_prefs_check, hcp_fs_check, hcp_postfs_check, hcp_bold_vol_check, hcp_bold_surf_check or hcp_dwi_check parameter for PreFreeSurfer, FreeSurfer, PostFreeSurfer, fMRIVolume, fMRISurface and Diffusion pipelines respectively. In addition, the user has to provide a document that specifies which files should be generated. These files are called "full file checking files". They are regular text files that list a path to each file that is expected to be created in a separate line. Paths should be specified relative to the hcp folder in which the processing is taking place. The character separating the individual parts of the path is space (" "). Empty lines and lines starting with # will be ignored.

The paths for some files can include session or scan specific information that will differ from session to session and scan to scan. These parts of the path are specified using variable placeholders. In places where the path is expected to contain session id, use {sessionid} placeholder. Use {scan} in places where the name of a file or folder is expected to contain the name of the specific scan.

If multiple options are possible and any of them satisfy the check, list them in the same line separated by the pipe | symbol.

The default names of files for the HCPpipelines processing steps are:

  • check_PreFreeSurfer.txt

  • check_FreeSurfer.txt

  • check_PostFreeSurfer.txt

  • check_fMRIVolume.txt

  • check_fMRISurface.txt

  • check_Diffusion.txt

These files will be looked for by default. Other file names can be used but in this case the full path to the file has to be specified in the relevant parameter.

Examples#

# check_PostFreeSurfer.txt segment

MNINonLinear aparc.a2009s+aseg.nii.gz
MNINonLinear aparc+aseg.nii.gz
MNINonLinear BiasField.nii.gz
MNINonLinear brainmask_fs.nii.gz
MNINonLinear fsaverage {sessionid}.L.def_sphere.164k_fs_L.surf.gii
MNINonLinear fsaverage {sessionid}.L.sphere.164k_fs_L.surf.gii
MNINonLinear fsaverage {sessionid}.R.def_sphere.164k_fs_R.surf.gii
MNINonLinear fsaverage {sessionid}.R.sphere.164k_fs_R.surf.gii
MNINonLinear fsaverage_LR32k {sessionid}.32k_fs_LR.wb.spec
MNINonLinear fsaverage_LR32k {sessionid}.aparc.32k_fs_LR.dlabel.nii
MNINonLinear fsaverage_LR32k {sessionid}.aparc.a2009s.32k_fs_LR.dlabel.nii
MNINonLinear fsaverage_LR32k {sessionid}.ArealDistortion_FS.32k_fs_LR.dscalar.nii
MNINonLinear fsaverage_LR32k {sessionid}.corrThickness.32k_fs_LR.dscalar.nii
MNINonLinear fsaverage_LR32k {sessionid}.curvature.32k_fs_LR.dscalar.nii
# check_fMRIVolume.txt segment

MNINonLinear Results {scan}
MNINonLinear Results {scan} {scan}_Jacobian.nii.gz
MNINonLinear Results {scan} {scan}_PhaseOne_gdc_dc.nii.gz
MNINonLinear Results {scan} {scan}_PhaseTwo_gdc_dc.nii.gz
MNINonLinear Results {scan} {scan}_SBRef.nii.gz
MNINonLinear Results {scan} {scan}.nii.gz
MNINonLinear Results {scan} brainmask_fs.2.nii.gz
MNINonLinear Results {scan} Movement_AbsoluteRMS_mean.txt
MNINonLinear Results {scan} Movement_AbsoluteRMS.txt
MNINonLinear Results {scan} Movement_Regressors_dt.txt
MNINonLinear Results {scan} Movement_Regressors.txt
MNINonLinear Results {scan} Movement_RelativeRMS_mean.txt
MNINonLinear Results {scan} Movement_RelativeRMS.txt
MNINonLinear xfms {scan}2standard.nii.gz
MNINonLinear xfms standard2{scan}.nii.gz

{scan} DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased FieldMap SBRef2PhaseTwo_gdc.mat    | {scan} DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased FieldMap SBRef2PhaseOne_gdc.mat
{scan} DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased FieldMap SBRef2PhaseTwo_gdc.nii.gz | {scan} DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased FieldMap SBRef2PhaseOne_gdc.nii.gz