# Outputs of fMRIPrep¶

FMRIPrep generates three broad classes of outcomes:

1. Visual QA (quality assessment) reports: one HTML per subject, that allows the user a thorough visual assessment of the quality of processing and ensures the transparency of fMRIPrep operation.

2. Pre-processed imaging data which are derivatives of the original anatomical and functional images after various preparation procedures have been applied. For example, INU-corrected versions of the T1-weighted image (per subject), the brain mask, or BOLD images after head-motion correction, slice-timing correction and aligned into the same-subject’s T1w space or into MNI space.

3. Additional data for subsequent analysis, for instance the transformations between different spaces or the estimated confounds.

fMRIPrep outputs conform to the BIDS Derivatives specification (see BIDS Derivatives RC1).

## Visual Reports¶

FMRIPrep outputs summary reports, written to <output dir>/fmriprep/sub-<subject_label>.html. These reports provide a quick way to make visual inspection of the results easy. Each report is self contained and thus can be easily shared with collaborators (for example via email). View a sample report.

## Preprocessed data (fMRIPrep derivatives)¶

Preprocessed, or derivative, data are written to <output dir>/fmriprep/sub-<subject_label>/. The BIDS Derivatives RC1 specification describes the naming and metadata conventions we follow.

Anatomical derivatives are placed in each subject’s anat subfolder:

• anat/sub-<subject_label>_[space-<space_label>_]desc-preproc_T1w.nii.gz

• anat/sub-<subject_label>_[space-<space_label>_]desc-brain_mask.nii.gz

• anat/sub-<subject_label>_[space-<space_label>_]dseg.nii.gz

• anat/sub-<subject_label>_[space-<space_label>_]label-CSF_probseg.nii.gz

• anat/sub-<subject_label>_[space-<space_label>_]label-GM_probseg.nii.gz

• anat/sub-<subject_label>_[space-<space_label>_]label-WM_probseg.nii.gz

Template-normalized derivatives use the space label MNI152NLin2009cAsym, while derivatives in the original T1w space omit the space- keyword.

Additionally, the following transforms are saved:

• anat/sub-<subject_label>_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5

• anat/sub-<subject_label>_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5

If FreeSurfer reconstructions are used, the following surface files are generated:

• anat/sub-<subject_label>_hemi-[LR]_smoothwm.surf.gii

• anat/sub-<subject_label>_hemi-[LR]_pial.surf.gii

• anat/sub-<subject_label>_hemi-[LR]_midthickness.surf.gii

• anat/sub-<subject_label>_hemi-[LR]_inflated.surf.gii

And the affine translation between T1w space and FreeSurfer’s reconstruction (fsnative) is stored in:

• anat/sub-<subject_label>_from-T1w_to-fsnative_mode-image_xfm.txt

Functional derivatives are stored in the func subfolder. All derivatives contain task-<task_label> (mandatory) and run-<run_index> (optional), and these will be indicated with [specifiers].

• func/sub-<subject_label>_[specifiers]_space-<space_label>_boldref.nii.gz

• func/sub-<subject_label>_[specifiers]_space-<space_label>_desc-brain_mask.nii.gz

• func/sub-<subject_label>_[specifiers]_space-<space_label>_desc-preproc_bold.nii.gz

Volumetric output spaces include T1w and MNI152NLin2009cAsym (default).

Confounds are saved as a TSV file:

• func/sub-<subject_label>_[specifiers]_desc-confounds_regressors.nii.gz

If FreeSurfer reconstructions are used, the (aparc+)aseg segmentations are aligned to the subject’s T1w space and resampled to the BOLD grid, and the BOLD series are resampled to the midthickness surface mesh:

• func/sub-<subject_label>_[specifiers]_space-T1w_desc-aparcaseg_dseg.nii.gz

• func/sub-<subject_label>_[specifiers]_space-T1w_desc-aseg_dseg.nii.gz

• func/sub-<subject_label>_[specifiers]_space-<space_label>_hemi-[LR].func.gii

Surface output spaces include fsnative (full density subject-specific mesh), fsaverage and the down-sampled meshes fsaverage6 (41k vertices) and fsaverage5 (10k vertices, default).

If CIFTI outputs are requested, the BOLD series is also saved as dtseries.nii CIFTI2 files:

• func/sub-<subject_label>_[specifiers]_bold.dtseries.nii

Sub-cortical time series are volumetric (supported spaces: MNI152NLin2009cAsym), while cortical time series are sampled to surface (supported spaces: fsaverage5, fsaverage6)

Finally, if ICA-AROMA is used, the MELODIC mixing matrix and the components classified as noise are saved:

• func/sub-<subject_label>_[specifiers]_AROMAnoiseICs.csv

• func/sub-<subject_label>_[specifiers]_desc-MELODIC_mixing.tsv

## FreeSurfer Derivatives¶

A FreeSurfer subjects directory is created in <output dir>/freesurfer.

freesurfer/
fsaverage{,5,6}/
mri/
surf/
...
sub-<subject_label>/
mri/
surf/
...
...


Copies of the fsaverage subjects distributed with the running version of FreeSurfer are copied into this subjects directory, if any functional data are sampled to those subject spaces.

## Confounds¶

See implementation on init_bold_confs_wf.

For each BOLD run processed with fMRIPrep, a <output_folder>/fmriprep/sub-<sub_id>/func/sub-<sub_id>_task-<task_id>_run-<run_id>_desc-confounds_regressors.tsv file will be generated. These are TSV tables, which look like the example below:

csf   white_matter    global_signal   std_dvars       dvars   framewise_displacement  t_comp_cor_00   t_comp_cor_01   t_comp_cor_02   t_comp_cor_03   t_comp_cor_04   t_comp_cor_05   a_comp_cor_00   a_comp_cor_01   a_comp_cor_02   a_comp_cor_03   a_comp_cor_04   a_comp_cor_05   non_steady_state_outlier00      trans_x trans_y trans_z rot_x   rot_y   rot_z   aroma_motion_02 aroma_motion_04
682.75275     0.0     491.64752000000004      n/a     n/a     n/a     0.0     0.0     0.0     0.0     0.0     0.0     0.0     0.0     0.0     0.0     0.0     0.0     1.0     0.0     0.0     0.0     -0.00017029     -0.0    0.0     0.0     0.0
669.14166     0.0     489.4421        1.168398        17.575331       0.07211929999999998     -0.4506846719   0.1191909139    -0.0945884724   0.1542023065    -0.2302324641   0.0838194238    -0.032426848599999995   0.4284323184    -0.5809158299   0.1382414008    -0.1203486637   0.3783661265    0.0     0.0     0.0207752       0.0463124       -0.000270924    -0.0    0.0     -2.402958171    -0.7574011893
665.3969      0.0     488.03  1.085204        16.323903999999995      0.0348966       0.010819676200000001    0.0651895837    -0.09556632150000001    -0.033148835    -0.4768871111   0.20641088559999998     0.2818768463    0.4303863764    0.41323714850000004     -0.2115232212   -0.0037154909000000004  0.10636180070000001     0.0     0.0     0.0     0.0457372       0.0     -0.0    0.0     -1.341359143    0.1636017242
662.82715     0.0     487.37302       1.01591 15.281561       0.0333937       0.3328022893    -0.2220965269   -0.0912891436   0.2326688125    0.279138129     -0.111878887    0.16901660629999998     0.0550480212    0.1798747037    -0.25383302620000003    0.1646403629    0.3953613889    0.0     0.010164        -0.0103568      0.0424513       0.0     -0.0    0.00019174      -0.1554834655   0.6451987913


Each row of the file corresponds to one time point found in the corresponding BOLD time-series (stored in <output_folder>/fmriprep/sub-<sub_id>/func/sub-<sub_id>_task-<task_id>_run-<run_id>_desc-preproc_bold.nii.gz).

Columns represent the different confounds: csf and white_matter are the average signal inside the anatomically-derived CSF and WM masks across time; global_signal corresponds to the mean time series within the brain mask; two columns relate to the derivative of RMS variance over voxels (or DVARS), and both the original (dvars) and standardized (std_dvars) are provided; framewise_displacement is a quantification of the estimated bulk-head motion; trans_x, trans_y, trans_z, rot_x, rot_y, rot_z are the 6 rigid-body motion-correction parameters estimated by fMRIPrep; if present, non_steady_state_outlier_XX columns indicate non-steady state volumes with a single 1 value and 0 elsewhere (i.e., there is one non_steady_state_outlier_XX column per outlier/volume); additional noise components are calculated using CompCor, according to both the anatomical (a_comp_cor_XX) and temporal (t_comp_cor_XX) variants; and the motion-related components identified by ICA-AROMA (if enabled) are indicated with aroma_motion_XX.

Four separate CompCor decompositions are performed to compute noise components: one temporal decomposition and three anatomical decompositions across three different noise ROIs: an eroded white matter compartment, an eroded CSF compartment, and a combined mask derived from the union of these. In general, only a subset of these decompositions should be used for further denoising. The original Behzadi aCompCor implementation ([Behzadi2007]) can be applied using components from the combined ROI, while the more recent Muschelli implementation ([Muschelli2014]) can be applied using the WM and CSF ROIs. To determine the provenance of each component, consult the metadata file (see below).

All these confounds can be used to perform scrubbing and censoring of outliers, in the subsequent first-level analysis when building the design matrix, and in group level analysis. Spike regressors for outlier censoring can also be generated from within fMRIPrep using the command line options --fd-spike-threshold and --dvars-spike-threshold. Spike regressors are stored in separate motion_outlier_XX columns.

Each confounds data file will also have a corresponding metadata file (~desc-confounds_regressors.json). Metadata files contain additional information about columns in the confounds TSV file:

{
"a_comp_cor_00": {
"CumulativeVarianceExplained": 0.1081970825,
"Method": "aCompCor",
"Retained": true,
"SingularValue": 25.8270209974,
"VarianceExplained": 0.1081970825
},
"dropped_0": {
"CumulativeVarianceExplained": 0.5965809597,
"Method": "aCompCor",
"Retained": false,
"SingularValue": 20.7955177198,
"VarianceExplained": 0.0701465624
}
}


For CompCor decompositions, entries include:

• Method: anatomical or temporal CompCor.

• Mask: denotes the ROI where the decomposition that generated the component was performed: CSF, WM, or combined for anatomical CompCor.

• SingularValue: singular value of the component.

• VarianceExplained: the fraction of variance explained by the component across the decomposition ROI mask.

• CumulativeVarianceExplained: the total fraction of variance explained by this particular component and all preceding components.

• Retained: Indicates whether the component was saved in desc-confounds_regressors.tsv for use in denoising. Entries that are not saved in the data file for denoising are still stored in metadata with the dropped prefix.

## Confounds and “carpet”-plot on the visual reports¶

Some of the estimated confounds, as well as a “carpet” visualization of the BOLD time-series (see [Power2016]). This plot is included for each run within the corresponding visual report. An example of these plots follows:

The figure shows on top several confounds estimated for the BOLD series: global signals (‘GlobalSignal’, ‘WM’, ‘GM’), standardized DVARS (‘stdDVARS’), and framewise-displacement (‘FramewiseDisplacement’). At the bottom, a ‘carpetplot’ summarizing the BOLD series. The colormap on the left-side of the carpetplot denotes signals located in cortical gray matter regions (blue), subcortical gray matter (orange), cerebellum (green) and the union of white-matter and CSF compartments (red).

Noise components computed during each CompCor decomposition are evaluated according to the fraction of variance that they explain across the nuisance ROI. This is used by fMRIPrep to determine whether each component should be saved for use in denoising operations: a component is saved if it contributes to explaining the top 50 percent of variance in the nuisance ROI. fMRIPrep can be configured to save all components instead using the command line option --return-all-components. fMRIPrep reports include a plot of the cumulative variance explained by each component, ordered by descending singular value.

The figure displays the cumulative variance explained by components for each of four CompCor decompositions (left to right: anatomical CSF mask, anatomical white matter mask, anatomical combined mask, temporal). The number of components is plotted on the abscissa and the cumulative variance explained on the ordinate. Dotted lines indicate the minimum number of components necessary to explain 50%, 70%, and 90% of the variance in the nuisance mask. By default, only the components that explain the top 50% of the variance are saved.

Also included is a plot of correlations among confound regressors. This can be used to guide selection of a confound model or to assess the extent to which tissue-specific regressors correlate with global signal.

The left-hand panel shows the matrix of correlations among selected confound time series as a heatmap. Note the zero-correlation blocks near the diagonal; these correspond to each CompCor decomposition. The right-hand panel displays the correlation of selected confound time series with the mean global signal computed across the whole brain; the regressors shown are those with greatest correlation with the global signal. This information can be used to diagnose partial volume effects.

References