The preprocessed resting state time series in MNI space can be found here: resting_state -> ants -> rest_mni_unsmoothed.nii.gz the same file with 6mm smoothing here: resting_state -> FWHM6 -> rest_mni_smoothed.nii

• ants EPI in MNI space
  • rest_mni_unsmoothed_fullspectrum.nii.gz preprocessed EPI in MNI space withouth BP filtering
  • rest_mni_unsmoothed.nii.gz preprocessed EPI in MNI space with BP filtering (0.01-0.1Hz)
• coregister
  • rest2anat.dat.mincost mincost file
  • rest_coregistered_nativespace.nii.gz
  • rest_mean2anat_highres.nii.gz unwarped epi registered to anatomy
  • rest_mean2anat_lowres.nii.gz
  • rest_mean2fmap.nii.gz
  • rest_mean2fmap_unwarped.nii.gz
  • T1_resampled.nii.gz
  • transforms2anat
    • B0_ph_fslprepared.nii.gz
    • fullwarpfield.nii.gz
    • rest2anat.dat transformation freesurfer format (fieldmap space to anatomy!)
    • rest2anat.mat transformation fsl format
• denoise
  • artefact rapidart output files (outliers, outlier plot, global intensity, composite norm, stats)
    • art.rest2anat_masked_outliers.txt
    • global_intensity.rest2anat_masked.txt
    • norm.rest2anat_masked.txt
    • plot.rest2anat_masked.png
    • stats.rest2anat_masked.txt
  • mask
    • T1_brain_mask2epi.nii.gz brain mask in original epi space (only for qa)
    • T1_brain_mask_lowres.nii.gz brain mask used during artefact detection and 2nd glm
    • wmcsf_mask_lowres.nii.gz white matter / csf mask used for acompcor
  • regress Nuisance Regression
    • F_mcart.nii.gz F-values of full model fit 1st glm
    • F_noise.nii.gz regressors 2nd glm
    • mcart_regressor.txt regressors 1st glm
    • noise_regressor.txt regressors 2nd glm
    • pF_mcart.nii.gz p-values for full model fit 1st glm
    • pF_noise.nii.gz F-values of full model fit 2nd glm
  • rest_preprocessed_nativespace_fullspectrum.nii.gz denoised EPI in native space withouth BP filtering
  • rest_preprocessed_nativespace.nii.gz **denoised EPI in native space with BP filtering (0.01-0.1Hz) **
• FWHM6
  • rest_mni_smoothed.nii.gz preprocessed EPI in MNI space with BP filtering (0.01-0.1Hz) and smoothing w 6mm
• realign
  • MAT realignment matrices for all volumes
    • MAT_0000
    • ....
    • MAT_0294
  • plots plots of estimated motion
    • abs_displacement_plot.png
    • rel_displacment_plot.png
    • rotation_plot.png
    • translation_plot.png
  • rest_realigned_abs.rms absolute and relative rms displacement (similar to mean frame displacement)
  • rest_realigned_mean.nii.gz temporal mean after realignment
  • rest_realigned.par realignment parameters
  • rest_realigned_rel.rms absolute and relative rms displacement (similar to mean frame displacement)
  • rest_realigned_tsnr.nii.gz temporal snr after realignment

• brain.nii.gz skull stripped
• T1_brain2mni.nii.gz brain in MNI152 1mm space
• T1_brain_mask.nii.gz brain mask
• T1.nii.gz whole head after background masking in freesurfer space
• transforms2mni transforms anatomy to MNI space (use antsApplyTransfom)
  • transform0GenericAffine.mat
  • transform1InverseWarp.nii.gz inverse of nonlinear transformation
  • transform1Warp.nii.gz