1.The FMRIB Software Library, abbreviated FSL, is a software library containing image analys and statistical tools for functional, structural and diffusion MRI brain imaging data.

2.What image format does FSL need?

FSL programs expect to read NIFTI-1 format images. These files can be read and written in compressed (gzip format) or uncompressed form. To convert between these different formats, use the fslchfiletype utility or the environment variable FSLOUTPUTTYPE. These are described more fully in the nifti1 page.

An image can be 2D or 3D or 4D (multiple time points).

FSL programs for FMRI analysis use single 4D NIFTI images, not lots of 3D images (such as SPM does).

3.How do I know right from left in the images?

Look at the labels in FSLView. For more information about orientation, the NIfTI format and FSLView display, see the "Orientation-related Utilities" and "Background information on NItTI Orientation" sections of the FSLUTILS documentation page (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Fslutils#Orientation-related_Utilities).

fslreorient2std - this is a simple tool designed to reorient an image to match the orientation of the standard template images (MNI152) so that they appear "the same way around" in FSLView. It requires that the image labels are correct in FSLView before this is run. It is also not a registration tool, so it will not align the image to standard space, it will only apply 90, 180 or 270 degree rotations about the different axes as necessary to get the labels in the same position as the standard template.

4.The NIfTI standard is confusing for many people, because that the intensity data is stored on  disk as a list of numbers - there is no concept of spatial or anatomical location with these numbers, and so information and standard conventions are used to associate spatial and anatomical location information with these numbers.

To start with, voxel coordinates are associated with the numbers (intensity values), such that the first number is at coordinate (0,0,0) the second at (1,0,0), the third at (2,0,0), etc. So, for example, say the image was 64 by 64 by 20 in size, then the coordinates would go as (0,0,0) then (1,0,0) ... then (63,0,0) then (0,1,0) then (1,1,0) then (2,1,0) ... then (63,1,0) then (0,2,0) ... then (63,63,0) then (0,0,1) then (1,0,1) ... until (63,63,19).

Having two matrices here is a common source of confusion. They were originally proposed so that two different coordinates could be kept track of - one representing the scanner coordinate system (the real space inside the scanner bore) and the other one relating to standard space coordinates (e.g. MNI152). However, in practice, it is rare that both contain different information as they are often set to be the same, or one of them is "Unknown" in which case the other contains all the useful information.

Either matrix (qform or sform) is used to convert the voxel coordinates into "real world" coordinates (also called continuous coordinates, or mm coordinates, or other names). These new coordinates - called (x,y,z) here

FSLView displays both voxel and mm coordinates

If the qform (or sform) is set so that it gives information about scanner coordinates (as indicated by the code), then a standard convention is used to relate the coordinate values to the anatomy. The convention is: +x = Right; +y = Anterior; +z = Superior. That is, moving in the positive x-direction (so that the x-coordinate increases) will be moving to the right, etc.

The information from the qform and sform is what is used by FSLView to determine the labels that are shown on the image

A valid NIfTI image can be displayed in any orientation that the viewing tool chooses, with the  left side of the brain shown on the right side of the screen (so called radiological convention) or the other way around (neurological convention). It is also possible to display the inferior side  of the brain at the top of the image, or any other configuration. It is entirely up to the display  software how it chooses to show the image on the screen. What the NIfTI format does do is  provide information to determine how to label the different parts of the image (with mm coordinates or anatomical labels such as left, right, anterior, posterior, superior and inferior)