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nipreps / smriprep

Structural MRI PREProcessing (sMRIPrep) workflows for NIPreps (NeuroImaging PREProcessing tools)

Home Page:https://nipreps.github.io/smriprep

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Fit/apply breakdown

effigies opened this issue · comments

commented

Ran sMRIPrep on one subject, checking off the proposed things to include in the minimal outputs:

  • sub-02_desc-aparcaseg_dseg.nii.gz
  • sub-02_desc-aseg_dseg.nii.gz
  • sub-02_desc-brain_mask.json
  • sub-02_desc-brain_mask.nii.gz
  • sub-02_desc-preproc_T1w.json
  • sub-02_desc-preproc_T1w.nii.gz
  • sub-02_dseg.nii.gz
  • sub-02_from-fsnative_to-T1w_mode-image_xfm.txt
  • sub-02_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
  • sub-02_from-T1w_to-fsnative_mode-image_xfm.txt
  • sub-02_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
  • sub-02_hemi-L_inflated.surf.gii
  • sub-02_hemi-L_midthickness.surf.gii
  • sub-02_hemi-L_pial.surf.gii
  • sub-02_hemi-L_smoothwm.surf.gii
  • sub-02_hemi-R_inflated.surf.gii
  • sub-02_hemi-R_midthickness.surf.gii
  • sub-02_hemi-R_pial.surf.gii
  • sub-02_hemi-R_smoothwm.surf.gii
  • sub-02_label-CSF_probseg.nii.gz
  • sub-02_label-GM_probseg.nii.gz
  • sub-02_label-WM_probseg.nii.gz
  • sub-02_space-MNI152NLin2009cAsym_desc-brain_mask.json
  • sub-02_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
  • sub-02_space-MNI152NLin2009cAsym_desc-preproc_T1w.json
  • sub-02_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz
  • sub-02_space-MNI152NLin2009cAsym_dseg.nii.gz
  • sub-02_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz
  • sub-02_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz
  • sub-02_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz

So we include:

  1. Merged and INU-corrected T1
  2. Brain mask
  3. dseg/probseg in T1 space
  4. Transforms

And we skip:

  1. FreeSurfer segmentations resampled into T1w space
  2. FreeSurfer surfaces converted to GIFTI and translated into T1w space
  3. All MNI-space outputs