Automatic Atlas Query
If you need a table with the coordinates and atlas labels of clusters in a nifti map, check out this script written by Brainder. In his words, any information that is not shared is lost, so I hope he doesn't mind me sharing his script here.Colorbars
To make colorbars for your figures when using fslview, navigate to: /usr/local/fsl/etc/luts (or wherever you save your FSL directory), and find colorbar.nii.gz. Open that file in fslview and you can change the colors to the ones matching your figure. Then screenshot the image.
fslorient2std
Very often, the files you obtained from the scanner are oriented in a weird way, and are incompatible with the MNI152 Standard Template Image used in registration. Use this command to reorient the image so that they appear the "same way round" in FSLVIEW (note, your original images do have to have the correct header information)
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