Clipping raster brick object in R

Question

1. I have MODIS NDVI TIFF files for a year
2. I want to first clip it with a irregular polygon (not by its extent only) of my study area and save it as a multi band raster in TIFF format The TIFF image are already projected to the needed coordinate system and datum (WGS 84, UTM 45N)
3. I used the writeRaster() function for the rasterbrick object but it gives me an error.
   If anyone has faced similar problems or could you suggest me better way doing this task.

   writeRaster(ndvit1, filename="ndvi_2015t1.tif", bandorder='BSQ', format="GTiff", overwrite=TRUE) Error in rgdal::putRasterData(x@file@transient, vv, band = i, offset = off) : Failure during raster IO In addition: Warning message: closing unused connection 4 (C:\Users\Ghimirebr\AppData\Local\Temp\RtmpwJschv\raster\r_tmp_2016-04-11_121550_3352_50703.gri)

## Clip a raster (brick) with the polygon (shape file) in its extent
## and mask value nan for the remaining area.

library(raster)
library(rgdal)

# Setting working directory:

setwd("C:/Working_Folder/R")
ndvi_path <- "ndvi_2015"

# Reading the shapefile 
myShapeInR <- readOGR("C:/working_folder/Boundary", 
                      "Chitwan_Nawal_Boundary")

# To view the summary of vector file
summary(myShapeInR)

# Getting the spatial extent of the shapefile 
e <- extent(myShapeInR) 

# Reading the raster you want to crop 
all_ndvi <- list.files(ndvi_path,
                       full.names = TRUE,
                       pattern = ".tif$")
ndvi_stack <- stack(all_ndvi)
ndvi_brick <- brick(ndvi_stack)

# Converting from -1 to 1 (NDVI)
ndvit1 <- ndvi_brick*0.0001

# Saving the RASTER BRICK
writeRaster(ndvit1, filename="ndvi_2015t1.tif", bandorder='BSQ',
            format="GTiff", overwrite=TRUE)
# myraster <- raster(myraster.filename) 

# Cropping the raster to the shapefile spatial extent 
ndvit1.crop <- crop(raster, e, snap="out") 

# Dummy raster with a spatial extension equal to the cropped raster, 
# but full of NA values 
crop <- setValues(ndvit1.crop, NA) 

# Rasterize the catchment boundaries, with NA outside the catchment boundaries 
myShapeInR.r <- rasterize(myShapeInR, crop) 

# Putting NA values in all the raster cells outside the shapefile boundaries 
ndvit1.masked <- mask(x=ndvit1.crop, mask=myShapeInR.r)

Answer 1

In order to write a raster stack or brick, the Interleave band can be used in the option argument.

    writeRaster(ndvi_stack, filename="<filename>.tif", options="INTERLEAVE=BAND", overwrite=TRUE)