# Minimal derivatives

sub-X/func/sub-X_task-Y_run-Z_desc-hmc_boldref.nii.gz  # BOLD contrast
sub-X/func/sub-X_task-Y_run-Z_desc-coreg_boldref.nii.gz  # aligned to hmcref, use sbref and fieldmaps, if possible
sub-X/func/sub-X_task-Y_run-Z_from-orig_to-boldref_mode-image_xfm.txt
sub-X/func/sub-X_task-Y_run-Z_from-boldref_to-T1w_mode-image_xfm.txt
sub-X/func/sub-X_task-Y_run-Z_from-T1w_to-boldref_mode-image_xfm.txt
sub-X/func/sub-X_task-Y_run-Z_from-fmap_to-boldref_mode-image_xfm.txt  # MI metric

## Dependency structure

graph TB;
    subgraph Head motion correction
    bold.nii --> desc-hmc_boldref.nii;
    bold.nii --> from-orig_to-boldref_xfm.txt;
    desc-hmc_boldref.nii-->from-orig_to-boldref_xfm.txt;
    end
    
    subgraph Bold reference selection
    sbref.nii--->desc-intermediate_boldref.nii;
    desc-hmc_boldref.nii-->desc-intermediate_boldref.nii;
    end
    
    subgraph Susceptibility Distortion Correction
    fmapref.nii---->from-fmap_to-boldref_xfm.txt;
    desc-intermediate_boldref.nii-->from-fmap_to-boldref_xfm.txt;
    fmap.nii----->space-boldref_fmap.nii;
    from-fmap_to-boldref_xfm.txt-->space-boldref_fmap.nii;
    space-boldref_fmap.nii-->desc-coreg_boldref.nii;
    end
    
    desc-intermediate_boldref.nii-->desc-coreg_boldref.nii;
    
    subgraph Coregistration
    T1w.nii -------> from-boldref_to-T1w_xfm.txt;
    desc-coreg_boldref.nii-->from-boldref_to-T1w_xfm.txt;
    end

graph TB;
    bold.nii & sbref.nii & T1w.nii & epi.nii & phasediff.nii & mangitude*.nii & fieldmap.nii --> sdcflows --> fmap.nii & fmapref.nii

# Application notes

graph TD;
    bold.nii -- slice-timing correction --> desc-stc_bold.nii;
    desc-stc_bold.nii -- split -->  idx-*_desc-stc_bold.nii;
    space-boldref_bold.nii --> desc-confounds_timeseries.tsv;
    idx-*_desc-stc_bold.nii -- resample and merge -->
    space-boldref_bold.nii & space-*_bold.nii & hemi-L_space-fsnative_bold.func.gii & hemi-R_space-fsnative_bold.func.gii;
    space-*_bold.nii -- select space-MNI152NLin6Asym ---> space-fsLR_bold.dtseries.nii;
    hemi-L_space-fsnative_bold.func.gii -- resample --> hemi-L_space-fsLR_bold.func.gii;
    hemi-R_space-fsnative_bold.func.gii -- resample --> hemi-R_space-fsLR_bold.func.gii;
    hemi-L_space-fsLR_bold.func.gii & hemi-R_space-fsLR_bold.func.gii
    --> space-fsLR_bold.dtseries.nii;

# Single-shot surface resampling changes

* Resample coordinates into boldref (Take GIFTIs in T1w space, apply `T1w->boldref` ITK transform (via nitransforms) to get surfaces in each boldref space.)
* In:
* GIFTI in T1w space (output of smriprep)
* `from-T1w_to-boldref_xfm`
* Out:
* GIFTI surface in boldref
* Resample fieldmap in Hz to surface
* In:
* Fieldmap to boldref transform
* GIFTI in boldref
* Out:
* Fieldmap (in Hz) on surface
* Resample BOLD with SDC+HMC onto surface
* Inputs:
* BOLD (STC if done)
* GIFTIs in boldref
* HMC transforms
* Fieldmap on surface
* Optional: weight values from `-volume-to-surface-mapping`
* Optional: goodvoxels mask
* Output
* fsnative BOLD

## Additional notes

* Generate reports 100% from derivatives directory
*