Hi Ben,
Have a look at MRIconvert which also outputs to .nii and works well.
Regards,
Benny
2010/5/24 Ben Yerys <[log in to unmask]>:
> Hi FSL experts--
>
> Our dicom script converts the images into analyze format and for some reason the MPRAGE image has a different orientation than the EPI data. The file does not have qform or sform set so I cannot use RL IS AP settings with fslswapdim. Using my eye, the correct orientation appears to be:
> fslswapdim <input> -z y x <output>, but I get the message that this command swaps the x dimension.
>
> When I run FEAT, the high_res to standard example image shows terrible alignment, and I'm guessing this is due to my swapdim commands being wrong. I tried to attach a screenshot of the raw MPRAGE image, but I couldn't make the total size of the image and message less than 50 k. I am willing to send separately or upload if pictures will help.
>
> I greatly appreciate your input!
>
> Best,
> Ben
>
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