Week of 5.15.23 to 5.19.23

• Freesurfer ingress + ABCD pipeline flow overhaul.

  • Testing the CPAC:abcd-prep preconfig > Freesurfer Recon-All > CPAC:abcd-options preconfig workflow succeeded in the hands of a test user, and the data processing ran smoothly.
  • Currently, we are assessing a poor-quality template-space BOLD mask resulting from one of these runs. It appears possible something is going awry in or around the native-space T1w brain mask warp to T1w template in the overwrite_transform_anat_to_template nodeblock.

• fmriprep ingress.

  • An existing function for BIDS sidecar JSON meta-data ingress was adapted to pull the TR information of ingressed BOLD data.
  • Decision was made to create a dedicated config entry for the template-space mask, to decouple the FSL-AFNI template entry from template-space nuisance regression.
    • (This coupling existed only within the develop branch during development).
  • The fmriprep confounds TSV features a wide range of regressors to choose from, so we realized functionality is needed to allow users to select which regressors from the fmriprep confounds they want to apply in nuisance correction. This is in-progress and will entail:
    • A change to the pipeline config taking in a list of column names for custom/ingressed regressor files.
    • A function node that checks that these column names actually exist in the regressors/confounds file.
    • Reading in the selected columns and re-writing out a new smaller confounds file for use with AFNI 3dTproject.
  • Currently on hold:
    • Functional data ingress iterables solution.
    • Storing space-* and resolution-* BIDS tags parsed from the already-preprocessed ingressed data, storing them in the meta-data, and re-applying to the final outputs as appropriate.

• Automation Testing: Correlation script was integrated to the regression test lite.

  • Testing the workflow for any crashes, but currently have only integrated the default pipeline for calculating correlations.

• Upgrade Dependencies: PR for branch upgrade/python is being reviewed and testing on ACCESS. One problem is that the branch container does not run using singularity. Currently reviewing what changes may have caused it to not run using singularity.

• fmriprep BOLD mask mapping

  • Traced the anatomical and functional working directories to identify the discrepancy between the CPAC run and the fmriprep run.
  • The bold to template mask creation step from CPAC and friprep was identified to be similar.

    • From fmriprep: antsApplyTransforms --default-value 0 --float 1 --input /ocean/projects/med220004p/tgeorge/Leonas_issue/work/fmriprep_2007_sub-PA048/fmriprep_wf/single_subject_PA048_wf/func_preproc_ses_V3W3_task_ovalfamily_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_trans_corrected_brain_mask_maths.nii.gz --interpolation MultiLabel --output ref_bold_corrected_trans_corrected_brain_mask_maths_trans.nii.gz --reference-image /ocean/projects/med220004p/tgeorge/Leonas_issue/work/fmriprep_2007_sub-PA048/fmriprep_wf/single_subject_PA048_wf/func_preproc_ses_V3W3_task_ovalfamily_wf/bold_t1_trans_wf/gen_ref/sub-PA048_ses-V3W3_acq-MPR_rec-vNavNorm_T1w_corrected_masked_xform_reference.nii.gz --transform /ocean/projects/med220004p/tgeorge/Leonas_issue/work/fmriprep_2007_sub-PA048/fmriprep_wf/single_subject_PA048_wf/func_preproc_ses_V3W3_task_ovalfamily_wf/bold_reg_wf/fsl_bbr_wf/fsl2itk_fwd/affine.txt

    • From CPAC: antsApplyTransforms --default-value 0 --float 0 --input /outputs/working/pipeline_default-fmriprep_fs-off_be-bet_seg-ants_despike-off_nightly/cpac_sub-PA048_ses-V3W3/_scan_ovalfamily/combine_masks_112/ref_bold_corrected_brain_mask_maths.nii.gz --interpolation MultiLabel --output ref_bold_corrected_brain_mask_maths_trans.nii.gz --reference-image /outputs/working/pipeline_default-fmriprep_fs-off_be-bet_seg-ants_despike-off_nightly/cpac_sub-PA048_ses-V3W3/resampled_T1w-brain-template-funcreg/T1w-brain-template-funcreg/tpl-MNI152NLin2009cAsym_res-02_T1w_reference_resample.nii.gz --transform /outputs/working/pipeline_default-fmriprep_fs-off_be-bet_seg-ants_despike-off_nightly/cpac_sub-PA048_ses-V3W3/ANTS_T1_to_template_58/write_composite_xfm/from-T1w_to-template_mode-image_xfm.nii.gz --transform /outputs/working/pipeline_default-fmriprep_fs-off_be-bet_seg-ants_despike-off_nightly/cpac_sub-PA048_ses-V3W3/_scan_ovalfamily/convert_bbr2itk_200/affine.txt

  The discrepancy between the two masks might be arising from the composite transforms created by the pipelines.