Preproc#

What images are resampled during preprocessing and to what resolution?#

In the spatial preprocessing workflow (bidsSpatialPrepro) called by bidspm(..., 'action', 'preprocess', ...):

  1. When no normalization is requested

This is the case when 'space', 'individual', functional images resolution is not changed. This cannot be overridden.

  1. During normalization to MNI

By default, functional images resolution is not changed. Override possible by setting opt.funcVoxelDims to the desired resolution.

The anatomical images are resampled at 1 mm.

Tissue probability maps downsampled at resolution of functional images mostly to help with potential with creation of tissue-based mask and also quality control pipelines.

For several files, you can guess their resolution if they have res entity in their filename:

  • res-bold means that the image is resampled at the resolution of the BOLD timeseries

  • res-r1pt0 means that the image is resampled at a resolution of 1.00 mm isometric

  sub-01
  ├── anat
  │   ├── sub-01_space-individual_desc-biascor_T1w.nii                   # native res
  │   ├── sub-01_space-individual_desc-skullstripped_T1w.nii             # native res
  │   ├── sub-01_space-individual_label-brain_mask.nii                   # native res
  │   ├── sub-01_space-individual_label-CSF_probseg.nii
  │   ├── sub-01_space-individual_label-GM_probseg.nii
  │   ├── sub-01_space-individual_label-WM_probseg.nii
  │   ├── sub-01_space-individual_res-r1pt0_desc-preproc_T1w.nii         # 1.0 mm
  │   ├── sub-01_space-IXI549Space_res-bold_label-CSF_probseg.nii        # bold res
  │   ├── sub-01_space-IXI549Space_res-bold_label-GM_probseg.nii         # bold res
  │   ├── sub-01_space-IXI549Space_res-bold_label-WM_probseg.nii         # bold res
  │   └── sub-01_space-IXI549Space_res-r1pt0_T1w.nii                     # 1.0 mm
  └── func
      ├── sub-01_task-auditory_space-individual_desc-mean_bold.nii       # native res
      ├── sub-01_task-auditory_space-individual_desc-preproc_bold.nii    # native res
      ├── sub-01_task-auditory_space-individual_desc-std_bold.nii        # native res
      ├── sub-01_task-auditory_space-IXI549Space_desc-mean_bold.nii      # native res
      └── sub-01_task-auditory_space-IXI549Space_desc-preproc_bold.nii   # native res

See those slides for some pointers on how to make choices for the resolution to choose for your analysis.

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