Package: neurobase 1.32.4
neurobase: 'Neuroconductor' Base Package with Helper Functions for 'nifti' Objects
Base package for 'Neuroconductor', which includes many helper functions that interact with objects of class 'nifti', implemented by package 'oro.nifti', for reading/writing and also other manipulation functions.
Authors:
neurobase_1.32.4.tar.gz
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neurobase_1.32.4.tgz(r-4.4-any)neurobase_1.32.4.tgz(r-4.3-any)
neurobase_1.32.4.tar.gz(r-4.5-noble)neurobase_1.32.4.tar.gz(r-4.4-noble)
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neurobase.pdf |neurobase.html✨
neurobase/json (API)
NEWS
| # Install 'neurobase' in R: |
| install.packages('neurobase', repos = c('https://muschellij2.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/muschellij2/neurobase/issues
Last updated 7 months agofrom:b343871251. Checks:OK: 5 NOTE: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 05 2024 |
| R-4.5-win | NOTE | Nov 05 2024 |
| R-4.5-linux | NOTE | Nov 05 2024 |
| R-4.4-win | OK | Nov 05 2024 |
| R-4.4-mac | OK | Nov 05 2024 |
| R-4.3-win | OK | Nov 05 2024 |
| R-4.3-mac | OK | Nov 05 2024 |
Exports:apply_empty_dimapplyEmptyImageDimensionsbreakercheck_maskcheck_mask_failcheck_nifticheck_nifti_headercheck_outfilecheckimgcheckniicheckniigzcogcolorbarcopyNIfTIHeaderdatatyperdicerdouble_orthodrop_empty_dimdropEmptyImageDimensionsempty_dim_maskemptyImageDimensionsMaskensure_arrayensure_niiensure_nii_gzfast_dicefast_dice_tabfast_readniifile_imgextfinite_imgflip_imgget_empty_dimgetEmptyImageDimensionsimages2matriximg_color_dfimg_colour_dfimg_indicesimg_list_to_tsimg_ts_to_dfimg_ts_to_listimg_ts_to_matrixis_rpi_orientedmask_empty_dimmask_imgmask_valsmask_vals<-maskEmptyImageDimensionsminmax_imgmulti_overlaymulti_overlay_centermulti_overlay_diffnewniiniftiarrnii.stuborient_rpiorient_rpi_fileortho_diffortho2parse_img_extquantile_imgrandom_niftirandomize_maskread_rpireadNIfTI2readniiremake_imgremap_filenamereplace_dropped_dimensionsreplace_empty_dimreplace_outside_surfacereplaceEmptyImageDimensionsrescale_imgreverse_orient_rpireverse_orient_rpi_filerobust_windowsame_dimsseparate_imgslice_colour_dfsubset_dtitempimgwindow_imgwrite_niftiwriteNIfTI2writeniixyzzero_padzlimmerzscore_img
Dependencies:abindbitopsmatrixStatsoro.niftiR.methodsS3R.ooR.utilsRcppRNifti
NIfTI Basics using the Eve atlas
Rendered fromneurobase.Rmdusingknitr::rmarkdownon Nov 05 2024.Last update: 2021-03-30
Started: 2017-01-31
Simple Image Input/Output
Rendered fromsimple_io.Rmdusingknitr::rmarkdownon Nov 05 2024.Last update: 2019-09-12
Started: 2019-09-12
The nifti object
Rendered fromnifti_basics.Rmdusingknitr::rmarkdownon Nov 05 2024.Last update: 2021-03-30
Started: 2016-12-08
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Apply Subsetting from Empty Image Dimensions | applyEmptyImageDimensions applyEmptyImageDimensions,anlz-method applyEmptyImageDimensions,ANY-method applyEmptyImageDimensions,array-method applyEmptyImageDimensions,character-method applyEmptyImageDimensions,factor-method applyEmptyImageDimensions,list-method applyEmptyImageDimensions,nifti-method applyEmptyImageDimensions-methods apply_empty_dim |
| Boxplot of Values in an Image | boxplot.anlz boxplot.nifti |
| Find Breaks for nifti Image Plotting | breaker |
| Check Mask is Binary | check_mask |
| Check Mask is Binary, Fail otherwise | check_mask_fail |
| Check if nifti image or read in a nifti header | check_nifti_header check_nifti_header,anlz-method check_nifti_header,ANY-method check_nifti_header,array-method check_nifti_header,character-method check_nifti_header,factor-method check_nifti_header,list-method check_nifti_header,nifti-method check_nifti_header-methods |
| Check if nifti image or read in a nifti image | check_nifti check_nifti,anlz-method check_nifti,ANY-method check_nifti,array-method check_nifti,character-method check_nifti,factor-method check_nifti,list-method check_nifti,nifti-method check_nifti-methods |
| Check output filename | check_outfile |
| Force object to filename | checkimg checkimg,ANY-method checkimg,character-method checkimg,list-method checkimg,nifti-method checkimg-methods |
| Force object to filename with .nii extension | checknii checknii,ANY-method checknii,character-method checknii,factor-method checknii,list-method checknii,nifti-method checknii-methods ensure_nii |
| Force object to filename with .nii.gz extension | checkniigz checkniigz,ANY-method checkniigz,character-method checkniigz,factor-method checkniigz,list-method checkniigz,nifti-method checkniigz-methods ensure_nii_gz |
| Image Center of Gravity | cog |
| Add a colorbar to an ortho2 object | colorbar |
| Copy NIfTI Header to an array | copyNIfTIHeader |
| Perform Cut on an image | cut.anlz cut.nifti |
| Change Data type for img | datatype datatyper |
| Density of Values in an Image | density.anlz density.nifti |
| Calculate Dice from a Table | dicer |
| Double Orthographic Display | double_ortho |
| Drop Empty Image Dimensions | dropEmptyImageDimensions drop_empty_dim |
| Make Mask from Empty Image Dimensions | emptyImageDimensionsMask empty_dim_mask |
| Ensure an array output | ensure_array |
| Fast Dice Tabulation | fast_dice fast_dice_tab |
| Reading NIfTI images through RNifti | fast_readnii |
| Get Image file extension | file_imgext |
| Finite Image | finite_img finite_img,ANY-method finite_img,array-method finite_img,character-method finite_img,list-method finite_img,nifti-method finite_img-methods |
| Flip NifTI Image | flip_img |
| Get Empty Image Dimensions | getEmptyImageDimensions get_empty_dim |
| Histogram of Values in an Image | hist.anlz hist.nifti |
| Transform set of images to matrix | images2matrix |
| Convert Image to Data.frame with Colors | img_color_df img_colour_df |
| Retrieve Image Indices | img_indices |
| Image List to Time Series | img_list_to_ts |
| Image Time Series to Data.frame | img_ts_to_df |
| Image Time Series to list | img_ts_to_list |
| Image Time Series to Matrix | img_ts_to_matrix |
| Mask Image | mask_img |
| Extract or Replace Values Inside a Mask | mask_vals mask_vals-methods, mask_vals<- mask_vals<-,anlz,ANY,ANY-method mask_vals<-,anlz-method mask_vals<-,array,ANY,ANY-method mask_vals<-,array-method mask_vals<-,nifti,ANY,ANY-method mask_vals<-,nifti-method |
| Apply Masking from Empty Image Dimensions | maskEmptyImageDimensions maskEmptyImageDimensions,anlz-method maskEmptyImageDimensions,ANY-method maskEmptyImageDimensions,array-method maskEmptyImageDimensions,character-method maskEmptyImageDimensions,factor-method maskEmptyImageDimensions,list-method maskEmptyImageDimensions,nifti-method maskEmptyImageDimensions-methods mask_empty_dim |
| Mean of Values in an Image | mean.anlz mean.nifti |
| Normalize Image using Range | minmax_img minmax_img,ANY-method minmax_img,array-method minmax_img,character-method minmax_img,factor-method minmax_img,list-method minmax_img,nifti-method minmax_img-methods |
| Create Multi-Image Plot with Overlays | multi_overlay multi_overlay_center |
| Resets image parameters for a copied nifti object | newnii |
| Make new nifti from array | niftiarr |
| Grab nii file stubname | nii.stub |
| Reorient an Image to RPI orientation | is_rpi_oriented orient_rpi orient_rpi_file |
| Plot differences for Prediction and Gold Standard | multi_overlay_diff ortho_diff |
| Orthographic Display, added options | ortho2 |
| Parse Image Extensions | parse_img_ext |
| Create Quantile Image | quantile_img |
| Sample Quantiles | quantile.anlz quantile.nifti |
| Create Random `nifti` object | random_nifti |
| Randomize Image based on Mask | randomize_mask |
| Read NIfTI file reoriented to RPI | read_rpi |
| readNIfTI with default non-reorientation | readNIfTI2 readnii |
| Remake Image from Vector | remake_img |
| Build Filename (usually for images) | remap_filename |
| Remake Dropped Dimensions | replace_dropped_dimensions |
| Replace Values Outside Surface of image | replace_outside_surface |
| Replace Subsetting from Empty Image Dimensions | replaceEmptyImageDimensions replaceEmptyImageDimensions,anlz-method replaceEmptyImageDimensions,ANY-method replaceEmptyImageDimensions,array-method replaceEmptyImageDimensions,character-method replaceEmptyImageDimensions,factor-method replaceEmptyImageDimensions,list-method replaceEmptyImageDimensions,nifti-method replaceEmptyImageDimensions-methods replace_empty_dim |
| Image Rescaler | rescale_img |
| Reverse Reorientation an Image to RPI orientation | reverse_orient_rpi reverse_orient_rpi_file |
| Window image based on quantiles of Image | robust_window |
| Check if Objects have Same Dimensions | same_dims |
| Separate Labeled Image into Multiple Binary Images | separate_img separate_img,ANY-method separate_img,array-method separate_img,character-method separate_img,factor-method separate_img,list-method separate_img,nifti-method separate_img-methods |
| Slice a Image Color Data.frame | slice_colour_df |
| Subset DTI data based on b-values #' | subset_dti subset_dti,ANY-method subset_dti,character-method subset_dti,list-method subset_dti,nifti-method subset_dti-methods |
| Create temporary nii.gz file | tempimg |
| nifti image windower | window_img |
| General NIfTI Writer | write_nifti |
| writeNIfTI with default non-reorientation | writeNIfTI2 writenii |
| Image Center of Gravity Wrapper | xyz |
| Zero pads an image | zero_pad |
| Find Image z-limits | zlimmer |
| Get Z-score over a margin of an img | zscore_img |
