BIDS formatted with ses level Freesurfer dir Training data
- Prepare template: uses smriprep-preprocessed template and creates distancemap and masks in template space of each subject
- Prepare T1w: Brings session T1w image into template space
- Prepare FLAIR: Brings t1w, distancemap and masks from template space into flair space. Runs biascorrection on flair images.
- Prepare Masterfile
- Run Bianca
Uses smriprep template to generate bianca masks and distancemap.
- smriprep t1w template is normalized with fsl
- results + CSF-pve are fed to
MakeBiancaMask - resulting ventricle mask is fed to
distancemap - distancemap is thresholded into perivent and deep WM (cut-off = 10mm)
creates a folder in prepare_template/sub-{subject}/anat/
All outputs (except space-MNI) are in smriprep template space.
| file | info |
|---|---|
| _desc-bianca_ventdistmap.nii.gz | distancemap from ventricles |
| _desc-bianca_ventmask.nii.gz | ventricle mask (MakeBiancaMask) |
| _desc-bianca_wmmask.nii.gz | WM Mask (MakeBiancaMask) |
| _desc-brain_mask.nii.gz | smriprep brain mask |
| _desc-deepWMmask.nii.gz | deep WM mask |
| _desc-periventmask.nii.gz | periventricular mask |
| _desc-preproc_T1w.nii.gz | preprocessed smriprep template |
| _from-tpl_to-MNI_warpfield.nii.gz | warp from template to MNI |
| _from-tpl_to-MNI_xfm.mat | transformation matrix from template to MNI |
| _space-MNI_desc-warped2mm.nii.gz | template in MNI space |
Bias corrects session T1w images, brings them to template space and averages them.
creates a folder in prepare_t1w/sub-{subject}/ses-{session}/anat/
that include files to be fed into prepare_flair (among other files):
| file | info |
|---|---|
| _space-tpl_T1w.nii.gz | preprocessed t1w |
| space-tpl_desc-brain_T1w.nii.gz | brain extracted preprocessed t1w |
- The flair image is bias corrected
- bring template-space images to flair space
- combine T1w-to-MNI registration (12 dof) with tpl-to-flair --> flair to MNI registration
creates a folder in prepare_flair/{acq}/sub-{subject}/ses-{session}/anat/ that includes:
for bianca:
| file | info | LOCATE |
|---|---|---|
| _FLAIR_biascorr.nii.gz | biascorrected flair | <subject_name>feature<base_modality_name>.nii.gz |
| _desc-12dof_from-{flairSpace}_to-MNI.mat | transformation matrix flair space to MNI | |
| _space-{flairSpace}_desc-t1w_brain.nii.gz | brain extracted t1w in flair space | <subject_name>feature<modality_name>.nii.gz |
| _space-{flairSpace}_desc-wmmask.nii.gz | wm mask in flair space |
for LOCATE:
| file | info | LOCATE |
|---|---|---|
| _space-{flairSpace}_desc-distanceVent.nii.gz | ventricular distance map | <subject_name>_ventdistmap.nii.gz |
| _space-{flairSpace}_desc-brainmask.nii.gz | brainmask | <subject_name>_brainmask.nii.gz |
| _space-{flairSpace}_desc-wmmask.nii.gz | wm mask | <subject_name>_biancamask.nii.gz |
misc:
| file | info |
|---|---|
| _space-MNI_desc-12dof_FLAIR.nii.gz | flair in mni space |
| _from-t1w_to-{flairSpace}.mat | transformation matrix t1w-tpl to flair space |
| _space-{flairSpace}_desc-deepWMmask.nii.gz | deep WM mask |
| _space-{flairSpace}_desc-periventmask.nii.gz | periventricular WM mask |
Creates a masterfile for bianca in {acq}/bianca
Runs bianca.
| file | info | LOCATE |
|---|---|---|
| _FLAIR_LPM.nii.gz | bianca lesion prob. mask | <subject_name>_BIANCA_LPM.nii.gz |
| _FLAIR_LPM.json | LPM information | |
| _FLAIR_classifier | classifier (if saved) | |
| _FLAIR_classifier_labels | classifier labels (if saved) |
LOCATE also needs the <subject_name>_manualmask.nii.gz
names files that can be used for locate (symlinks)
masks bianca LPM with bianca-wm-mask and applies threshold(s).
Runs bianca_cluster_stats
if run_BiancaOverlapMeasures=True, runs bianca_overlap_measures vs manual masks
| file | info |
|---|---|
| _FLAIR_desc-biancamasked.nii.gz | bianca LPM masked with bianca-wm-mask |
| _FLAIR_desc-thresh{threshold}_biancaLPMmaskedThrBin.nii.gz | bianca LPM masked with bianca-wm-mask, thresholdedand binarized |
| _FLAIR_desc-thresh{threshold}_ClusterStatsTotal.txt | output of bianca_cluster_stats bianca LPM masked with bianca-wm-mask |
| _FLAIR_desc-thresh{threshold}_ClusterStatsdeepwm.txt | output of bianca_cluster_stats within deep wm mask (bianca LPM masked with bianca-wm-mask) |
| _FLAIR_desc-thresh{threshold}_ClusterStatsperventwm.txt | output of bianca_cluster_stats within perivent wm mask (bianca LPM masked with bianca-wm-mask) |
| _FLAIR_desc-thresh{threshold}_overlap.txt | output of bianca_overlap_measures (bianca LPM masked with bianca-wm-mask) |
takes binary outputs from locate and applies bianca-wm-mask again (due to some resampling within locate, locate labels some voxels outside the bianca-wm-mask).