brainprep.interfaces: Module that implements interfaces.

Module that implements interfaces.

Functions

affine(anatomical_file, template_file, ...)	Affinely register a BIDS-compliant anatomical image to a template file using FSL's flirt.
anonfile(input_file, mapping)	Anonymize a text file using sed.
applyaffine(image_file, template_file, ...)	Apply an affine transformation to a BIDS-compliant image file using FSL's flirt.
applymask(image_file, mask_file, output_dir, ...)	Apply an isotropic resampling transformation to a BIDS-compliant image file using FSL's fslmaths.
biasfield(image_file, mask_file, output_dir, ...)	Bias field correction of a BIDS-compliant anatomical image using ANTs's N4BiasFieldCorrection.
brainmask(image_file, output_dir, entities)	Skull-strip a BIDS-compliant anatomical image using FreeSurfer's mri_synthstrip.
cat12vbm_morphometry(output_dir[, dryrun])	Extract ROI-based morphometry features and global tissue volumes from CAT12 VBM outputs.
cat12vbm_wf(t1_files, batch_file, ...)	Compute VBM prep-processing using CAT12.
copyfiles(source_image_files, ...[, dryrun])	Copy input image files.
deface(t1_file, output_dir, entities)	Defaces a BIDS-compliant T1-weighted anatomical image using FSL's fsl_deface.
euler_numbers(output_dir[, euler_threshold, ...])	FreeSurfer recon-all quality control.
fmriprep_metrics(output_dir[, ...])	FMRIprep quality control.
fmriprep_wf(t1_file, func_files, ...)	Compute fMRI prep-processing using fMRIPrep.
freesurfer_command_status(log_file, command)	Check the status of a FreeSurfer recon-all process from its log file.
freesurfer_features_summary(workspace_dir, ...)	Summarizes the generated FreeSurfer features for all subjects.
freesurfer_tissues(workspace_dir, ...[, ...])	Binary masks for white matter (WM), gray matter (GM), cerebrospinal fluid (CSF), and whole brain based on FreeSurfer ribbon and wmparc segmentations.
fsaveragesym_projection(left_reg_file, ...)	Project the different cortical features to the 'fsaverage_sym' template space using FreeSurfer's mris_apply_reg.
fsaveragesym_surfreg(output_dir, entities)	Interhemispheric surface-based registration using the fsaverage_sym template, and FreeSurfer's xhemireg and surfreg.
func_vol_connectivity(fmri_rest_image_file, ...)	ROI-based functional connectivity from volumetric fMRI data.
group_level_qa(modalities, output_dir)	Compute group level Image Quality Metrics (IQMs) generated by MRIQC.
incremental_pca(image_files_regex, output_dir)	Perform an Incremental PCA with 2 components on a collection of images matched by a regex pattern, processing them in batches.
localgi(output_dir, entities)	Local Gyrification Index (localGI or lGI).
mask_overlap(maskdiff_files_regex, output_dir)	Compute overlap ratios between mask pairs from maskdiff summary files.
maskdiff(mask1_file, mask2_file, output_dir, ...)	Compute summary statistics comparing two binary masks.
mean_correlation(image_files_regex, ...[, ...])	Compute the mean Pearson correlation between a reference image and a list of other images.
mgz_to_nii(output_dir, entities)	Convert FreeSurfer images back to original Nifti space.
movedir(source_dir, output_dir[, content, ...])	Move input directory.
mriqc_metrics(iqm_files, output_dir[, dryrun])	Filter MRIQC group-level metrics according to modality-specific defaults.
network_entropy(network_files_regex, output_dir)	Comput enetwork entropy - "structure vs randomness" metric.
nextbrain(t1_file, output_dir, entities)	Uses NextBrain probabilistic atlas of the human brain, to segment ~300 distinct ROIs per hemisphere.
plot_brainparc(wm_mask_file, gm_mask_file, ...)	Parameters:
plot_defacing_mosaic(im_file, mask_file, ...)	Generates a defacing mosaic image by overlaying a mask on an anatomical image.
plot_histogram(table_file, col_name, output_dir)	Generates a histogram image with optional vertical bars.
plot_network(network_file, output_dir, entities)	Plot the given network using nilearn.
plot_pca(pca_file, output_dir[, dryrun])	Plot the two first PCA components.
reconall(t1_file, output_dir, entities[, ...])	Brain parcellation using FreeSurfer's recon-all.
reconall_longitudinal(workspace_dir, ...)	Longitudinal brain parcellation using FreeSurfer's recon-all.
reorient(image_file, output_dir, entities)	Reorients a BIDS-compliant anatomical image using FSL's fslreorient2std.
scale(image_file, scale, output_dir, entities)	Apply an isotropic resampling transformation to a BIDS-compliant image file using FSL's flirt.
subject_level_qa(image_files, workspace_dir, ...)	Compute subject level Image Quality Metrics (IQMs) generated by MRIQC.
ungzfile(input_file, output_file, output_dir)	Ungzip input file.
vbm_metrics(output_dir[, ncr_threshold, ...])	CAT12 VBM quality control.
write_catbatch(t1_files, output_dir, entities)	Generate CAT12 batch file.
write_uuid_mapping(input_file, output_dir, ...)	Create a TSV file that records a deterministic UUID-based mapping.