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I have a few MODIS products and as I was combining my imges I realised that some of the pixels around the coastline where abit off.Is that a standard issue and if so should I use reproject or should I georeference them on another image.And if I have to georeference those two images, should I use ArcGIS or ERDAS (I would like purely your opinion on the last question because I just wanted to know which one does this community prefer)

The Products that I am using are from MYD13Q1(AQUA) and MOD13Q1(TERRA) and the problem isn't just on the coastlines, it is also on every lake of the image.

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I suggest using the MODIS Reprojection Tool (MRT) to properly project your MODIS data. This might solve your alignment issue. Make sure you use the same coordinate system for each file. You can also mosaic tiles and convert HDF to GeoTIFF through its interface. Once you've done that, you can manipulate them further in ArcGIS or ERDAS.

Does the alignment issue exist when you bring the raw HDF files into ArcMap?

https://lpdaac.usgs.gov/tools/modis_reprojection_tool

MRT can be a bit finicky. You need to have both MRT and Java installed to a folder on your drive without spaces. I suggest reinstalling (or installing) Java and MRT to C:/programs/java and C:/programs/MRT. It can have problems searching for them when they are located in Program Files.

Note that the projection parameters default to the northern hemisphere. If you need another projection, you can reproject in another software package later. There is also an option to batch process your data by creating a parameter file. There are instructions on how to do that in the user manual (page 40). Also, if you add two scenes (or more) from the same day to the input files, it will mosaic them for you.

https://lpdaac.usgs.gov/sites/default/files/public/mrt41_usermanual_032811.pdf

MODIS Reprojection Tool

MODIS Reprojection Tool - Projection Parameters

  • So I don't really need to georeference my images?Great! P.S I forgot to mention that my files are in .img format. – George Nostradamos Jul 31 '16 at 13:27
  • Sounds like you've got some preprocessed data, which might not have been processed properly. MRT wont help with that. Was the data you downloaded from a NASA site? If you want to work with the original files you can download them from the NASA Reverb web portal. You can use MRT with the original HDF files. You won't need to do any georeferencing. If the data are summarized across a large time range it might be quicker to georeference and snap raster but you'll need to be careful that no resampling is done. I suggest using the raw data so you can be sure of your results. – cartoscience Jul 31 '16 at 15:13
  • My data were downloaded from USGS (earthexplorer) inf .hdf format but I to exported the EVI and the NDVI bands, with a little help from ERDAS, in .img format. – George Nostradamos Jul 31 '16 at 15:47
  • I see. I would check to see if the original HDFs are aligned (you can open them in ArcMap), then use MRT to project and convert the HDFs. MRT is specifically designed for MODIS data and skipping this step can cause some problems. – cartoscience Jul 31 '16 at 15:55
  • So I did what you said but something is wrong. I am going to put this out there by asking : my files are in .hdf.ecw is there a way to convert my files with ArcMap or ERDAS in hdf or do I have to download the same files from NASA? – George Nostradamos Jul 31 '16 at 16:17

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