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.git-keywords nf: testing git-keywords Feb 6, 2018
.git-rcs-keywords rf: testing two methods of RCS keyword expansion Feb 6, 2018
.github create an issue template to direct users Oct 16, 2017
BrainstemSS bf: make sure fs binaries called from matlab link to system libstdc++ Mar 1, 2019
GEMS2
HippoSF bf: make sure fs binaries called from matlab link to system libstdc++ Mar 1, 2019
ThalamicNuclei
anatomicuts Add -Wextra (#639) Mar 18, 2019
check_siemens_dir refactor codebase to c++ Feb 27, 2019
cmake
cnn-aseg-demo cnn aseg demo Feb 6, 2018
connectgraph refactor codebase to c++ Feb 27, 2019
deeplearn_utils adding deep learning utils Nov 23, 2017
diabetes remove dos line breaks (#620) Jan 29, 2019
diffusion_tool bf: update Qt5 cmake Jan 8, 2019
distribution
dmri_poistats
dmri_tensoreig
dngtester
docs
dummy refactor codebase to c++ Feb 27, 2019
dummy_qt
fem_elastic
freeview Fixed compile error Mar 18, 2019
fsfast
fslutils
hiam_make_surfaces refactor codebase to c++ Feb 27, 2019
hiam_make_template refactor codebase to c++ Feb 27, 2019
hiam_register
histo_compute_joint_density refactor codebase to c++ Feb 27, 2019
histo_fix_topology
histo_register remove dos line breaks (#620) Jan 29, 2019
histo_register_block
histo_segment
histo_synthesize refactor codebase to c++ Feb 27, 2019
include
infant remove dos line breaks (#620) Jan 29, 2019
itkio
itkutils refactor codebase to c++ Feb 27, 2019
label2flat refactor codebase to c++ Feb 27, 2019
label2patch refactor codebase to c++ Feb 27, 2019
label_area
label_border refactor codebase to c++ Feb 27, 2019
lineprof Updated code to build against both vtk5 and vtk8 Feb 26, 2019
lta_convert
matlab
mkxsubjreg
mri_add_xform_to_header
mri_and
mri_annotation2label refactor codebase to c++ Feb 27, 2019
mri_aparc2aseg Add -Wextra (#639) Mar 18, 2019
mri_aparc2wmseg
mri_apply_inu_correction refactor codebase to c++ Feb 27, 2019
mri_aseg_edit_reclassify
mri_aseg_edit_train refactor codebase to c++ Feb 27, 2019
mri_auto_fill
mri_average refactor codebase to c++ Feb 27, 2019
mri_bc_sc_bias_correct
mri_bias refactor codebase to c++ Feb 27, 2019
mri_binarize
mri_build_priors refactor codebase to c++ Feb 27, 2019
mri_ca_label
mri_ca_normalize
mri_ca_register refactor codebase to c++ Feb 27, 2019
mri_ca_register_test Make this available to other machines Dec 21, 2017
mri_ca_tissue_parms refactor codebase to c++ Feb 27, 2019
mri_ca_train refactor codebase to c++ Feb 27, 2019
mri_cal_renormalize_gca
mri_cc
mri_cc_ma_fill
mri_cc_medial_axis
mri_cht2p refactor codebase to c++ Feb 27, 2019
mri_classify refactor codebase to c++ Feb 27, 2019
mri_cnr
mri_compile_edits
mri_compute_change_map
mri_compute_overlap refactor codebase to c++ Feb 27, 2019
mri_compute_seg_overlap
mri_compute_structure_transforms
mri_compute_volume_fractions
mri_concat refactor codebase to c++ Feb 27, 2019
mri_concatenate_gcam
mri_concatenate_lta
mri_convert
mri_convert_mdh
mri_copy_values refactor codebase to c++ Feb 27, 2019
mri_cor2label
mri_coreg refactor codebase to c++ Feb 27, 2019
mri_correct_segmentations
mri_cvs_register repository maintenance (#617) Jan 17, 2019
mri_dct_align
mri_deface refactor codebase to c++ Feb 27, 2019
mri_diff refactor codebase to c++ Feb 27, 2019
mri_distance_transform refactor codebase to c++ Feb 27, 2019
mri_divide_segmentation
mri_edit_segmentation
mri_edit_segmentation_with_surfaces
mri_edit_wm_with_aseg refactor codebase to c++ Feb 27, 2019
mri_elastic_energy
mri_em_register refactor codebase to c++ Feb 27, 2019
mri_estimate_tissue_parms refactor codebase to c++ Feb 27, 2019
mri_evaluate_morph
mri_extract refactor codebase to c++ Feb 27, 2019
mri_extract_conditions refactor codebase to c++ Feb 27, 2019
mri_extract_fcd_features
mri_extract_label refactor codebase to c++ Feb 27, 2019
mri_extract_largest_CC
mri_extract_ma_intensity
mri_fcili
mri_fdr
mri_fieldsign
mri_fill refactor codebase to c++ Feb 27, 2019
mri_fit_bias refactor codebase to c++ Feb 27, 2019
mri_fslmat_to_lta
mri_fuse_intensity_images refactor codebase to c++ Feb 27, 2019
mri_fuse_segmentations refactor codebase to c++ Feb 27, 2019
mri_fwhm refactor codebase to c++ Feb 27, 2019
mri_gca_ambiguous
mri_gcab_train
mri_gcut refactor codebase to c++ Feb 27, 2019
mri_gdfglm
mri_glmfit Fixed bug from previous commit. Added more checks to flag problems wi… Mar 7, 2019
mri_gtmpvc
mri_gtmseg refactor codebase to c++ Feb 27, 2019
mri_hausdorff_dist
mri_head refactor codebase to c++ Feb 27, 2019
mri_hires_register refactor codebase to c++ Feb 27, 2019
mri_histo_eq
mri_histo_normalize
mri_ibmc
mri_iic
mri_info
mri_interpolate refactor codebase to c++ Feb 27, 2019
mri_jacobian
mri_joint_density
mri_label2label refactor codebase to c++ Feb 27, 2019
mri_label2vol refactor codebase to c++ Feb 27, 2019
mri_label_accuracy refactor codebase to c++ Feb 27, 2019
mri_label_histo refactor codebase to c++ Feb 27, 2019
mri_label_vals
mri_label_volume refactor codebase to c++ Feb 27, 2019
mri_linear_register
mri_log_likelihood
mri_make_bem_surfaces
mri_make_density_map
mri_make_labels refactor codebase to c++ Feb 27, 2019
mri_make_register
mri_make_template refactor codebase to c++ Feb 27, 2019
mri_map_atrophy bf: fix progname (#515) Sep 4, 2018
mri_map_cpdat refactor codebase to c++ Feb 27, 2019
mri_mark_temporal_lobe refactor codebase to c++ Feb 27, 2019
mri_mask
mri_matrix_multiply
mri_mc refactor codebase to c++ Feb 27, 2019
mri_mcsim
mri_mi
mri_modify
mri_morphology
mri_mosaic
mri_ms_EM
mri_ms_EM_with_atlas
mri_ms_LDA
mri_ms_fitparms refactor codebase to c++ Feb 27, 2019
mri_multiscale_segment
mri_multispectral_segment
mri_nlfilter refactor codebase to c++ Feb 27, 2019
mri_normalize
mri_normalize_tp2
mri_otl
mri_paint
mri_parse_sdcmdir refactor codebase to c++ Feb 27, 2019
mri_parselabel
mri_partial_ribbon refactor codebase to c++ Feb 27, 2019
mri_path2label refactor codebase to c++ Feb 27, 2019
mri_polv
mri_probe_ima refactor codebase to c++ Feb 27, 2019
mri_probedicom
mri_rbvpvc refactor codebase to c++ Feb 27, 2019
mri_reduce refactor codebase to c++ Feb 27, 2019
mri_refine_seg refactor codebase to c++ Feb 27, 2019
mri_register
mri_relabel_hypointensities
mri_relabel_nonwm_hypos
mri_remove_neck
mri_rf_label
mri_rf_long_label
mri_rf_long_train
mri_rf_train
mri_ribbon
mri_rigid_register refactor codebase to c++ Feb 27, 2019
mri_robust_register
mri_sbbr
mri_seg_diff refactor codebase to c++ Feb 27, 2019
mri_seg_overlap refactor codebase to c++ Feb 27, 2019
mri_segcentroids
mri_seghead
mri_segment refactor codebase to c++ Feb 27, 2019
mri_segment_tumor refactor codebase to c++ Feb 27, 2019
mri_segment_wm_damage refactor codebase to c++ Feb 27, 2019
mri_segreg refactor codebase to c++ Feb 27, 2019
mri_segstats refactor codebase to c++ Feb 27, 2019
mri_simulate_atrophy
mri_stats2seg
mri_strip_nonwhite
mri_strip_subject_info
mri_surf2surf
mri_surf2vol refactor codebase to c++ Feb 27, 2019
mri_surfacemask
mri_surfcluster
mri_synthesize refactor codebase to c++ Feb 27, 2019
mri_tessellate
mri_threshold
mri_topologycorrection refactor codebase to c++ Feb 27, 2019
mri_train refactor codebase to c++ Feb 27, 2019
mri_train_autoencoder refactor codebase to c++ Feb 27, 2019
mri_transform refactor codebase to c++ Feb 27, 2019
mri_transform_to_COR
mri_twoclass refactor codebase to c++ Feb 27, 2019
mri_update_gca refactor codebase to c++ Feb 27, 2019
mri_vol2roi
mri_vol2surf
mri_vol2vol
mri_volcluster refactor codebase to c++ Feb 27, 2019
mri_voldiff
mri_volsynth refactor codebase to c++ Feb 27, 2019
mri_warp_convert refactor codebase to c++ Feb 27, 2019
mri_watershed
mri_wbc refactor codebase to c++ Feb 27, 2019
mri_wmfilter
mri_xcorr refactor codebase to c++ Feb 27, 2019
mri_xvolavg refactor codebase to c++ Feb 27, 2019
mri_z2p
mris2rgb
mris_BA_segment refactor codebase to c++ Feb 27, 2019
mris_add_template
mris_anatomical_stats
mris_annot_to_segmentation refactor codebase to c++ Feb 27, 2019
mris_apply_reg refactor codebase to c++ Feb 27, 2019
mris_aseg_distance refactor codebase to c++ Feb 27, 2019
mris_average_curvature refactor codebase to c++ Feb 27, 2019
mris_average_parcellation
mris_ca_label
mris_ca_train refactor codebase to c++ Feb 27, 2019
mris_calc
mris_classify_thickness refactor codebase to c++ Feb 27, 2019
mris_compute_acorr
mris_compute_lgi remove dos line breaks (#620) Jan 29, 2019
mris_compute_optimal_kernel
mris_compute_overlap refactor codebase to c++ Feb 27, 2019
mris_compute_parc_overlap Add -Wextra (#639) Mar 18, 2019
mris_compute_volume_fractions
mris_congeal refactor codebase to c++ Feb 27, 2019
mris_convert
mris_copy_header
mris_curvature
mris_curvature_stats
mris_curvature_vectors
mris_decimate refactor codebase to c++ Feb 27, 2019
mris_defects_pointset refactor codebase to c++ Feb 27, 2019
mris_deform
mris_density
mris_diff
mris_distance_map refactor codebase to c++ Feb 27, 2019
mris_distance_to_label
mris_distance_transform refactor codebase to c++ Feb 27, 2019
mris_divide_parcellation
mris_entropy
mris_errors refactor codebase to c++ Feb 27, 2019
mris_euler_number refactor codebase to c++ Feb 27, 2019
mris_expand
mris_extract_patches refactor codebase to c++ Feb 27, 2019
mris_fbirn_annot refactor codebase to c++ Feb 27, 2019
mris_fill refactor codebase to c++ Feb 27, 2019
mris_find_flat_regions
mris_fix_topology regenerate testdata (related to PR #635) Mar 15, 2019
mris_fix_topology_test Bf deterministic parallel 3 (#256) Jan 24, 2018
mris_flatten refactor codebase to c++ Feb 27, 2019
mris_fwhm refactor codebase to c++ Feb 27, 2019
mris_glm refactor codebase to c++ Feb 27, 2019
mris_hausdorff_dist refactor codebase to c++ Feb 27, 2019
mris_inflate refactor codebase to c++ Feb 27, 2019
mris_info Added function MRISprintVertexInfo(). Similar to MRISprintVertexStats() Mar 13, 2019
mris_init_global_tractography
mris_interpolate_warp refactor codebase to c++ Feb 27, 2019
mris_jacobian
mris_label2annot refactor codebase to c++ Feb 27, 2019
mris_label_area
mris_label_calc
mris_label_mode refactor codebase to c++ Feb 27, 2019
mris_left_right_register
mris_longitudinal_surfaces
mris_make_average_surface refactor codebase to c++ Feb 27, 2019
mris_make_face_parcellation refactor codebase to c++ Feb 27, 2019
mris_make_map_surfaces
mris_make_surfaces bf: MRIScomputeBorderValues arguments Mar 21, 2019
mris_make_template refactor codebase to c++ Feb 27, 2019
mris_map_cuts
mris_merge_parcellations
mris_mesh_subdivide
mris_morph_stats
mris_ms_refine refactor codebase to c++ Feb 27, 2019
mris_ms_surface_CNR refactor codebase to c++ Feb 27, 2019
mris_multiscale_stats refactor codebase to c++ Feb 27, 2019
mris_niters2fwhm refactor codebase to c++ Feb 27, 2019
mris_parcellate_connectivity
mris_pmake bf: get mris_pmake building Feb 28, 2019
mris_pval_fill
mris_register refactor codebase to c++ Feb 27, 2019
mris_register_label_map
mris_register_to_volume
mris_remove_variance refactor codebase to c++ Feb 27, 2019
mris_resample
mris_rescale
mris_reverse
mris_rf_label refactor codebase to c++ Feb 27, 2019
mris_rf_train
mris_rotate refactor codebase to c++ Feb 27, 2019
mris_sample_label
mris_sample_parc
mris_seg2annot
mris_segment
mris_segment_vals refactor codebase to c++ Feb 27, 2019
mris_segmentation_stats refactor codebase to c++ Feb 27, 2019
mris_shrinkwrap refactor codebase to c++ Feb 27, 2019
mris_simulate_atrophy refactor codebase to c++ Feb 27, 2019
mris_smooth refactor codebase to c++ Feb 27, 2019
mris_smooth_intracortical bf: no GLOB_PERIOD on osx Mar 21, 2019
mris_spharm refactor codebase to c++ Feb 27, 2019
mris_sphere refactor codebase to c++ Feb 27, 2019
mris_spherical_average refactor codebase to c++ Feb 27, 2019
mris_spherical_wavelets
mris_surface_change refactor codebase to c++ Feb 27, 2019
mris_surface_stats refactor codebase to c++ Feb 27, 2019
mris_surface_to_vol_distances
mris_svm_classify refactor codebase to c++ Feb 27, 2019
mris_svm_train refactor codebase to c++ Feb 27, 2019
mris_talairach refactor codebase to c++ Feb 27, 2019
mris_thickness refactor codebase to c++ Feb 27, 2019
mris_thickness_comparison refactor codebase to c++ Feb 27, 2019
mris_thickness_diff refactor codebase to c++ Feb 27, 2019
mris_topo_fixer refactor codebase to c++ Feb 27, 2019
mris_transform
mris_translate_annotation
mris_transmantle_dysplasia_paths
mris_twoclass
mris_volmask
mris_volume refactor codebase to c++ Feb 27, 2019
mris_w_to_curv
mris_warp refactor codebase to c++ Feb 27, 2019
mris_watershed
mrisp_paint
mrisp_write
nmovie repository maintenance (#617) Jan 17, 2019
nmovie_qt
oct_register_mosaic
oct_train refactor codebase to c++ Feb 27, 2019
optseq2 refactor codebase to c++ Feb 27, 2019
packages
psacnn_brain_segmentation
pyScout cmake (#493) Aug 17, 2018
python nf psacnn release (#637) Mar 13, 2019
qdec
qdec_glmfit refactor codebase to c++ Feb 27, 2019
qdecproject refactor codebase to c++ Feb 27, 2019
qt bf: osx qt deployment Jan 8, 2019
rbftest refactor codebase to c++ Feb 27, 2019
regdat2xfm
repair_siemens_file refactor codebase to c++ Feb 27, 2019
resurf
samseg
scripts
spherical_stats refactor codebase to c++ Feb 27, 2019
spline3
stat_normalize
stim_polar refactor codebase to c++ Feb 27, 2019
swi_processing refactor codebase to c++ Feb 27, 2019
talairach_afd
talairach_avi rf: port test framework to bash Jan 25, 2019
template
test_makevol refactor codebase to c++ Feb 27, 2019
tkregister2 refactor codebase to c++ Feb 27, 2019
tktools
travis samseg integration (#512) Aug 30, 2018
trc Add -Wextra (#639) Mar 18, 2019
tridec
utils
vtkutils Fixed compile error with lastest VTK Mar 20, 2019
.clang-format clang-format tweaks Oct 11, 2017
.gitattributes
.gitconfig rf: testing two methods of RCS keyword expansion Feb 6, 2018
.gitignore
.travis.yml
CMakeLists.txt
Dockerfile [REF] don't clone freesurfer, only copy necessary files Feb 6, 2018
Doxyfile I think that static members should be documented too.... Mar 3, 2010
LICENSE.txt
README.md
references.txt
test.sh

README.md

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