'Neuroconductor' Base Package with Helper Functions for 'nifti'
Objects
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Documentation for package ‘neurobase’ version 1.32.3
Help Pages
A B C D E F G H I M N O P Q R S T W X Z
-- A --
| applyEmptyImageDimensions | Apply Subsetting from Empty Image Dimensions |
| applyEmptyImageDimensions-method | Apply Subsetting from Empty Image Dimensions |
| applyEmptyImageDimensions-methods | Apply Subsetting from Empty Image Dimensions |
| apply_empty_dim | Apply Subsetting from Empty Image Dimensions |
-- B --
| boxplot.anlz | Boxplot of Values in an Image |
| boxplot.nifti | Boxplot of Values in an Image |
| breaker | Find Breaks for nifti Image Plotting |
-- C --
| checkimg | Force object to filename |
| checkimg-method | Force object to filename |
| checkimg-methods | Force object to filename |
| checknii | Force object to filename with .nii extension |
| checknii-method | Force object to filename with .nii extension |
| checknii-methods | Force object to filename with .nii extension |
| checkniigz | Force object to filename with .nii.gz extension |
| checkniigz-method | Force object to filename with .nii.gz extension |
| checkniigz-methods | Force object to filename with .nii.gz extension |
| check_mask | Check Mask is Binary |
| check_mask_fail | Check Mask is Binary, Fail otherwise |
| check_nifti | Check if nifti image or read in a nifti image |
| check_nifti-method | Check if nifti image or read in a nifti image |
| check_nifti-methods | Check if nifti image or read in a nifti image |
| check_nifti_header | Check if nifti image or read in a nifti header |
| check_nifti_header-method | Check if nifti image or read in a nifti header |
| check_nifti_header-methods | Check if nifti image or read in a nifti header |
| check_outfile | Check output filename |
| cog | Image Center of Gravity |
| colorbar | Add a colorbar to an ortho2 object |
| copyNIfTIHeader | Copy NIfTI Header to an array |
| cut.anlz | Perform Cut on an image |
| cut.nifti | Perform Cut on an image |
-- D --
| datatype | Change Data type for img |
| datatyper | Change Data type for img |
| density.anlz | Density of Values in an Image |
| density.nifti | Density of Values in an Image |
| dicer | Calculate Dice from a Table |
| double_ortho | Double Orthographic Display |
| dropEmptyImageDimensions | Drop Empty Image Dimensions |
| drop_empty_dim | Drop Empty Image Dimensions |
-- E --
| emptyImageDimensionsMask | Make Mask from Empty Image Dimensions |
| empty_dim_mask | Make Mask from Empty Image Dimensions |
| ensure_array | Ensure an array output |
| ensure_nii | Force object to filename with .nii extension |
| ensure_nii_gz | Force object to filename with .nii.gz extension |
-- F --
| fast_dice | Fast Dice Tabulation |
| fast_dice_tab | Fast Dice Tabulation |
| fast_readnii | Reading NIfTI images through RNifti |
| file_imgext | Get Image file extension |
| finite_img | Finite Image |
| finite_img-method | Finite Image |
| finite_img-methods | Finite Image |
| flip_img | Flip NifTI Image |
-- G --
| getEmptyImageDimensions | Get Empty Image Dimensions |
| get_empty_dim | Get Empty Image Dimensions |
-- H --
| hist.anlz | Histogram of Values in an Image |
| hist.nifti | Histogram of Values in an Image |
-- I --
| images2matrix | Transform set of images to matrix |
| img_color_df | Convert Image to Data.frame with Colors |
| img_colour_df | Convert Image to Data.frame with Colors |
| img_indices | Retrieve Image Indices |
| img_list_to_ts | Image List to Time Series |
| img_ts_to_df | Image Time Series to Data.frame |
| img_ts_to_list | Image Time Series to list |
| img_ts_to_matrix | Image Time Series to Matrix |
| is_rpi_oriented | Reorient an Image to RPI orientation |
-- M --
| maskEmptyImageDimensions | Apply Masking from Empty Image Dimensions |
| maskEmptyImageDimensions-method | Apply Masking from Empty Image Dimensions |
| maskEmptyImageDimensions-methods | Apply Masking from Empty Image Dimensions |
| mask_empty_dim | Apply Masking from Empty Image Dimensions |
| mask_img | Mask Image |
| mask_vals | Extract or Replace Values Inside a Mask |
| mask_vals-methods, | Extract or Replace Values Inside a Mask |
| mask_vals<- | Extract or Replace Values Inside a Mask |
| mask_vals<--method | Extract or Replace Values Inside a Mask |
| mean.anlz | Mean of Values in an Image |
| mean.nifti | Mean of Values in an Image |
| minmax_img | Normalize Image using Range |
| minmax_img-method | Normalize Image using Range |
| minmax_img-methods | Normalize Image using Range |
| multi_overlay | Create Multi-Image Plot with Overlays |
| multi_overlay_center | Create Multi-Image Plot with Overlays |
| multi_overlay_diff | Plot differences for Prediction and Gold Standard |
-- N --
| newnii | Resets image parameters for a copied nifti object |
| niftiarr | Make new nifti from array |
| nii.stub | Grab nii file stubname |
-- O --
| orient_rpi | Reorient an Image to RPI orientation |
| orient_rpi_file | Reorient an Image to RPI orientation |
| ortho2 | Orthographic Display, added options |
| ortho_diff | Plot differences for Prediction and Gold Standard |
-- P --
| parse_img_ext | Parse Image Extensions |
-- Q --
| quantile.anlz | Sample Quantiles |
| quantile.nifti | Sample Quantiles |
| quantile_img | Create Quantile Image |
-- R --
| randomize_mask | Randomize Image based on Mask |
| random_nifti | Create Random 'nifti' object |
| readNIfTI2 | readNIfTI with default non-reorientation |
| readnii | readNIfTI with default non-reorientation |
| read_rpi | Read NIfTI file reoriented to RPI |
| remake_img | Remake Image from Vector |
| remap_filename | Build Filename (usually for images) |
| replaceEmptyImageDimensions | Replace Subsetting from Empty Image Dimensions |
| replaceEmptyImageDimensions-method | Replace Subsetting from Empty Image Dimensions |
| replaceEmptyImageDimensions-methods | Replace Subsetting from Empty Image Dimensions |
| replace_dropped_dimensions | Remake Dropped Dimensions |
| replace_empty_dim | Replace Subsetting from Empty Image Dimensions |
| replace_outside_surface | Replace Values Outside Surface of image |
| rescale_img | Image Rescaler |
| reverse_orient_rpi | Reverse Reorientation an Image to RPI orientation |
| reverse_orient_rpi_file | Reverse Reorientation an Image to RPI orientation |
| robust_window | Window image based on quantiles of Image |
-- S --
| same_dims | Check if Objects have Same Dimensions |
| separate_img | Separate Labeled Image into Multiple Binary Images |
| separate_img-method | Separate Labeled Image into Multiple Binary Images |
| separate_img-methods | Separate Labeled Image into Multiple Binary Images |
| slice_colour_df | Slice a Image Color Data.frame |
| subset_dti | Subset DTI data based on b-values #' |
| subset_dti-method | Subset DTI data based on b-values #' |
| subset_dti-methods | Subset DTI data based on b-values #' |
-- T --
| tempimg | Create temporary nii.gz file |
-- W --
| window_img | nifti image windower |
| writeNIfTI2 | writeNIfTI with default non-reorientation |
| writenii | writeNIfTI with default non-reorientation |
| write_nifti | General NIfTI Writer |
-- X --
| xyz | Image Center of Gravity Wrapper |
-- Z --
| zero_pad | Zero pads an image |
| zlimmer | Find Image z-limits |
| zscore_img | Get Z-score over a margin of an img |