T1 and T2 -weighed images

One individual report per input structural volume will be generated in the path <output_dir>/reports/sub-IDxxx_T1w.html`. An example report is given here.

The individual report for the structural images is structured as follows:


The first section summarizes some important information:

  • subject identifier, date and time of execution of mriqc, software version;

  • workflow details and flags raised during execution; and

  • the extracted IQMs.

Visual reports

The section with visual reports contains:

  1. Mosaic view, zoomed-in over the parenchyma of the brain.

    zoomed in mosaic
  2. Mosaic view with background noise enhancement.

    t1 background

Verbose reports

If mriqc was run with the --verbose-reports flag, the following plots will be appended:

  1. Mosaic view with animation for assessment of the co-registration to MNI space (roll over the image to activate the animation).

    t1-mni coregistration
  2. Three rows of axial views at different Z-axis points showing: the calculated brain mask, the segmentation done with FSL FAST and a saturated view of the background.

    t1 verbose masks 1
  3. Two rows of coronal views, showing the object/background segmentation, and the air/no-air segmentation.

    t1 verbose masks 2
  4. The \(\chi^2\) function fitting for the calculation of the QI2:

    t1 fitting of QI2


If some metadata was found in the BIDS structure, it is reported here.