fslreorient2std <input_image> [output_image]

[yinkaiming1987]

Dear John,

Could function fslreorient2std() has both the input_image and output_image? It seems now fslreorient2std() only accept one file as the input.

fslreorient2std.help()
Usage: fslreorient2std <input_image> [output_image] fslreorient2std is a tool for reorienting the image to match theapproximate orientation of the standard template images (MNI152).It only applies 0, 90, 180 or 270 degree rotations.It is not a registration tool.It requires NIfTI images with valid orientation informationin them (seen by valid labels in FSLView). This toolassumes the labels are correct - if not, fix that before using this.If the output name is not specified the equivalent transformation matrix is written to the standard output

fslreorient2std()
Error in checkimg(file, ...) :
argument "file" is missing, with no default

Thanks,
Kaiming

[muschellij2]

This request does not make sense with FSL syntax. fslreorient2std takes in an input file and outfile argument. Therefore, in fslr, there is an input and output. In FSL, it changes the file in place.

[yinkaiming1987]

Dear John,

So I just need to run:

Image2 <- fslreorient2std(file = image1)

And the changes will be kept in Image2 here, am I right?

Thanks,
Kaiming

On 8 April 2016 at 14:22, John Muschelli notifications@github.com wrote:

This request does not make sense with FSL syntax. fslreorient2std takes
in an input file and outfile argument. Therefore, in fslr, there is an
input and output. In FSL, it changes the file in place.

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#5 (comment)

[muschellij2]

Correct.