# 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.

In general, FMRIPREP follows the current working draft of the BIDS-derivatives extension.

## 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)¶

There are additional files, called “Derivatives”, written to <output dir>/fmriprep/sub-<subject_label>/. See the BIDS Derivatives spec for more information.

Derivatives related to T1w files are in the anat subfolder:

• *T1w_brainmask.nii.gz Brain mask derived using ANTs’ antsBrainExtraction.sh.
• *T1w_class-CSF_probtissue.nii.gz
• *T1w_class-GM_probtissue.nii.gz
• *T1w_class-WM_probtissue.nii.gz tissue-probability maps.
• *T1w_dtissue.nii.gz Tissue class map derived using FAST.
• *T1w_preproc.nii.gz Bias field corrected T1w file, using ANTS’ N4BiasFieldCorrection
• *T1w_space-MNI152NLin2009cAsym_brainmask.nii.gz Same as _brainmask above, but in MNI space.
• *T1w_space-MNI152NLin2009cAsym_class-CSF_probtissue.nii.gz
• *T1w_space-MNI152NLin2009cAsym_class-GM_probtissue.nii.gz
• *T1w_space-MNI152NLin2009cAsym_class-WM_probtissue.nii.gz Probability tissue maps, transformed into MNI space
• *T1w_space-MNI152NLin2009cAsym_dtissue.nii.gz Same as _dtissue above, but in MNI space
• *T1w_space-MNI152NLin2009cAsym_preproc.nii.gz Same as _preproc above, but in MNI space
• *T1w_space-MNI152NLin2009cAsym_target-T1w_warp.h5 Composite (warp and affine) transform to map from MNI to T1 space
• *T1w_target-MNI152NLin2009cAsym_warp.h5 Composite (warp and affine) transform to transform T1w into MNI space
• (optional) *T1w_target-fsnative_affine.txt Affine transform to transform T1w into fsnative space
• (optional) *T1w_smoothwm.[LR].surf.gii Smoothed GrayWhite surfaces
• (optional) *T1w_pial.[LR].surf.gii Pial surfaces
• (optional) *T1w_midthickness.[LR].surf.gii MidThickness surfaces
• (optional) *T1w_inflated.[LR].surf.gii FreeSurfer inflated surfaces for visualization

Derivatives related to EPI files are in the func subfolder.

• *bold_confounds.tsv A tab-separated value file with one column per calculated confound and one row per timepoint/volume
• (optional) *bold_AROMAnoiseICs.csv A comma-separated value file listing each MELODIC component classified as noise
• (optional) *bold_MELODICmix.tsv A tab-separated value file with one column per MELODIC component

Volumetric output spaces include T1w and MNI152NLin2009cAsym (default).

• *bold_space-<space>_brainmask.nii.gz Brain mask for EPI files, calculated by nilearn on the average EPI volume, post-motion correction
• *bold_space-<space>_preproc.nii.gz Motion-corrected (using MCFLIRT for estimation and ANTs for interpolation) EPI file
• (optional) *bold_space-<space>_variant-smoothAROMAnonaggr_preproc.nii.gz Motion-corrected (using MCFLIRT for estimation and ANTs for interpolation), smoothed (6mm), and non-aggressively denoised (using AROMA) EPI file - currently produced only for the MNI152NLin2009cAsym space

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

• (optional) *bold_space-<space>.[LR].func.gii Motion-corrected EPI file sampled to surface <space>

## 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>_confounds.tsv file will be generated. These are TSV tables, which look like the example below:

WhiteMatter GlobalSignal    stdDVARS    non-stdDVARS    vx-wisestdDVARS FramewiseDisplacement   tCompCor00  tCompCor01  tCompCor02  tCompCor03  tCompCor04  tCompCor05  aCompCor00  aCompCor01  aCompCor02  aCompCor03  aCompCor04  aCompCor05  NonSteadyStateOutlier00 X   Y   Z   RotX    RotY    RotZ    AROMAAggrComp01 AROMAAggrComp03 AROMAAggrComp04 AROMAAggrComp05
0.63    2.72    n/a n/a n/a n/a 0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    1.00    0.00    0.00    0.00    0.00    0.00    0.00    2.62    -1.12   -0.03   3.12
3.14    0.51    1.18    16.05   1.21    0.07    -0.21   -0.36   -0.23   0.29    -0.37   0.04    -0.33   -0.54   -0.36   0.22    -0.07   0.16    0.00    0.00    0.02    0.05    0.00    0.00    0.00    1.66    -1.74   -0.38   -0.99
-1.23   -0.85   1.09    14.86   1.11    0.03    0.02    0.04    -0.22   -0.08   -0.18   0.66    0.11    -0.45   -0.16   -0.28   -0.05   0.26    0.00    0.00    0.00    0.05    0.00    0.00    0.00    0.35    -1.22   0.10    -0.23
-1.61   -1.53   1.01    13.83   1.05    0.03    0.27    0.21    -0.07   0.21    0.30    -0.02   0.24    -0.15   0.24    0.17    0.51    -0.02   0.00    0.01    -0.01   0.04    0.00    0.00    0.00    -0.42   -0.55   0.49    -0.38
-3.43   -1.48   0.98    13.32   1.02    0.03    0.06    0.49    0.24    -0.18   0.06    0.12    0.25    0.11    0.09    -0.10   0.08    0.47    0.00    0.02    -0.01   0.03    0.00    0.00    0.00    -1.12   -0.40   0.21    1.23
0.71    -0.66   0.97    13.26   1.02    0.04    -0.29   0.43    0.14    0.06    -0.20   -0.32   0.40    0.22    -0.07   0.45    -0.02   -0.04   0.00    0.02    -0.02   0.03    0.00    0.00    0.00    -1.00   -0.91   -0.99   0.30
-2.81   0.61    0.95    12.98   1.01    0.08    -0.48   0.24    -0.11   -0.15   -0.16   -0.22   0.38    0.20    -0.35   0.16    -0.31   -0.01   0.00    0.00    0.00    0.05    0.00    0.00    0.00    -0.66   -0.49   -1.89   0.43
2.85    0.35    0.95    12.99   1.01    0.04    -0.22   0.00    -0.50   0.05    0.15    0.14    0.30    -0.20   -0.22   -0.22   0.04    -0.34   0.00    0.00    -0.01   0.03    0.00    0.00    0.00    0.01    0.22    -1.76   -0.39
-2.57   -0.54   1.04    14.22   1.07    0.05    0.45    0.01    -0.43   -0.51   -0.01   -0.20   0.13    -0.02   0.26    -0.62   0.00    -0.30   0.00    0.00    0.00    0.06    0.00    0.00    0.00    0.60    1.59    0.05    -0.46
3.41    -0.72   1.03    14.04   1.05    0.07    0.37    0.06    0.08    0.55    -0.21   -0.14   -0.10   -0.18   0.51    0.17    -0.24   0.05    0.00    0.00    0.02    0.07    0.00    0.00    0.00    0.52    0.71    1.63    -0.95
3.75    -0.54   1.01    13.83   1.04    0.06    0.16    -0.16   0.38    -0.19   -0.01   0.16    -0.11   0.18    0.37    0.00    -0.43   0.20    0.00    0.00    0.00    0.06    0.00    0.00    0.00    -0.53   -0.07   1.85    -0.01
0.41    1.19    1.05    14.28   1.08    0.06    -0.27   -0.38   0.32    -0.11   0.10    0.07    -0.31   0.31    -0.25   -0.24   -0.01   0.27    0.00    0.00    0.01    0.09    0.00    0.00    0.00    -0.75   -0.03   0.14    -0.26
-4.14   0.72    0.97    13.20   1.01    0.03    -0.13   -0.28   0.03    -0.16   0.48    -0.28   -0.26   0.40    -0.24   -0.10   0.18    -0.20   0.00    0.00    0.00    0.08    0.00    0.00    0.00    -0.44   1.03    -0.50   -0.15
2.21    -0.02   0.96    13.09   1.00    0.01    0.18    -0.26   -0.04   0.14    -0.05   -0.37   -0.26   -0.10   0.07    0.25    -0.10   -0.54   0.00    0.00    0.00    0.08    0.00    0.00    0.00    0.28    1.54    0.12    -0.77
0.08    -0.06   0.95    12.89   0.99    0.01    0.15    -0.12   0.31    -0.22   -0.37   0.08    -0.22   0.12    -0.02   0.01    -0.15   -0.10   0.00    0.00    0.00    0.08    0.00    0.00    0.00    -0.46   1.00    0.70    0.08
-1.41   0.29    0.96    13.06   0.99    0.01    -0.04   0.07    0.10    0.31    0.47    0.27    -0.22   0.09    0.11    0.12    0.56    0.14    0.00    0.00    0.00    0.07    0.00    0.00    0.00    -0.67   0.44    0.25    -0.57


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>_bold_preproc.nii.gz).

Columns represent the different confounds: CSF and WhiteMatter are the average signal inside the CSF and WM mask across time; GlobalSignal corresponds to the global-signal within the whole-brain mask; three columns relate to the derivative of RMS variance over voxels (or DVARS) that can be standardized (stdDVARS), non-standardized (non-stdDVARS), and voxel-wise standardized (vx-wisestdDVARS); the FrameDisplacement is a quantification of the estimated bulk-head motion; X, Y, Z, RotX, RotY, RotZ are the actual 6 rigid-body transform parameters estimated by FMRIPREP; the NonSteadyStateOutlier00 column is 1 when a non-steady state was found (typically at the beginning of the scan) and 0 elsewhere; and finally six noise components aCompCorXX calculated using CompCor and five noise components AROMAaggrCompXX if ICA-AROMA was enabled.

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.