Index

A

addr() (neural.dicom.DicomInfo method) affine_align() (in module neural.alignment) affine_apply() (in module neural.alignment) afni_copy() (in module neural.dsets)

align_epi() (in module neural.alignment) align_epi_anat() (in module neural.alignment) archive_basename() (in module neural.utils) auto_polort() (in module neural.dsets) available_method() (in module wrappers.common)

B

Beacon (class in neural.utils) blank_stim() (neural.decon.DeconStim method)

blur() (in module wrappers.common) bounding_box() (in module neural.dsets)

C

calc() (in module wrappers.common) cdf() (in module wrappers.common) check_packet() (neural.utils.Beacon method) classify() (in module neural.dicom) cluster() (in module wrappers.common) cluster_files() (in module neural.dicom) command_list() (neural.decon.Decon method) command_string() (neural.decon.Decon method)

compress() (in module neural.utils) concat_stim() (neural.decon.DeconStim method) connectivity_map() (in module neural.connectivity) convert_coord() (in module neural.alignment) coord (class in neural.driver) create_censor_file() (in module neural.preprocess) create_dset() (in module neural.dicom) create_dset_to3d() (in module neural.dicom)

D

date_for_image() (in module neural.dicom) date_for_str() (in module neural.dicom) decompress() (in module neural.utils) Decon (class in neural.decon) DeconStim (class in neural.decon) DicomInfo (class in neural.dicom)

dir_name (neural.freesurfer.FreesurferDir attribute) driver_send() (in module neural.driver) dset (class in neural.driver) dset_copy() (in module neural.dsets) dset_grids_equal() (in module neural.dsets) dset_info() (in module neural.dsets) DsetInfo (class in neural.dsets)

E

exists() (neural.utils.Beacon method)

F

factor() (in module neural.utils) find() (in module neural.utils)

find_dups() (in module neural.dicom) flatten() (in module neural.utils) FreesurferDir (class in neural.freesurfer)

G

guess_home() (in module neural.freesurfer)

H

hash() (in module neural.utils)

hash_str() (in module neural.utils)

I

ijk_to_xyz() (in module neural.dsets) info() (in module neural.dicom) info_for_tags() (in module neural.dicom) is_afni() (in module neural.dsets)

is_archive() (in module neural.utils) is_dicom() (in module neural.dicom) is_dset() (in module neural.dsets) is_nifti() (in module neural.dsets)

L

label() (neural.dicom.DicomInfo method)

log() (in module neural.utils)

M

mask_average() (in module neural.stats) max() (in module neural.stats) max_diff() (in module neural.dicom)

method_prefs (in module wrappers.common) mgz_to_nifti() (in module neural.freesurfer) motion_from_params() (in module neural.alignment)

N

neural.alignment (module) neural.connectivity (module) neural.decon (module) neural.dicom (module) neural.driver (module) neural.dsets (module)

neural.eprime (module) neural.freesurfer (module) neural.preprocess (module) neural.stats (module) neural.utils (module) nifti_copy() (in module neural.dsets) numberize() (in module neural.utils)

O

organize_dir() (in module neural.dicom)

P

parpar_dir() (in module neural.freesurfer) parse_frames() (in module neural.eprime) partial() (neural.decon.DeconStim method)

pkg_available() (in module wrappers.common) pkg_prefs (in module wrappers.common) prefix() (in module neural.dsets)

Q

qwarp_align() (in module neural.alignment) qwarp_apply() (in module neural.alignment)

qwarp_epi() (in module neural.alignment) qwarp_invert() (in module neural.alignment)

R

random_string() (in module neural.utils) read_file() (neural.decon.DeconStim method) read_header() (in module neural.eprime) recon_all() (in module neural.freesurfer) reconstruct_files() (in module neural.dicom) resample_dset() (in module neural.dsets)

roi_stats() (in module wrappers.common) run() (in module neural.utils) (neural.decon.Decon method) (neural.utils.Beacon method) run_in (class in neural.utils) run_in_tmp (class in neural.utils) RunResult (class in neural.utils)

S

save_image() (in module neural.driver) scan_dir() (in module neural.dicom) segment() (in module wrappers.common) set_thresh() (in module neural.driver) setup_freesurfer() (in module neural.freesurfer) simple_timer (class in neural.utils) skull_strip (neural.freesurfer.FreesurferDir attribute) skull_strip() (in module wrappers.common) skullstrip_template() (in module neural.alignment)

smooth_decon_to_fwhm() (in module neural.decon) sphere_average() (in module neural.stats) stack_decon_stims() (in module neural.decon) strip_rows() (in module neural.utils) strip_subbrick() (in module neural.dsets) subbrick() (in module neural.dsets) subj_dir (neural.freesurfer.FreesurferDir attribute) subj_id (neural.freesurfer.FreesurferDir attribute) suffix() (in module neural.dsets)

T

temp_afni_copy (class in neural.dsets) thread_safe() (neural.utils.Beacon method) ThreadSafe (class in neural.utils)

thresh() (in module wrappers.common) tshift() (in module wrappers.common) type() (neural.decon.DeconStim method)

U

unarchive() (in module neural.utils)

universal_read() (in module neural.utils) unpack_archive() (in module neural.dicom)

V

value_at_coord() (in module neural.dsets)

volreg() (in module neural.alignment) voxel_count() (in module neural.stats)

W

which() (in module neural.utils)

wrappers.common (module)

X

xhairs (class in neural.driver)