Take away the negative sign in front of the z to get rid of the message.
That being said, using analyze format is a bad idea because you lose left
right information. Do you use some fiducial marker (e.g. Vitamin E) to tell
which is right and which is left when you scan? If not, it might be a
better idea to use a program that converts directly from DICOM to NFITI like
dcm2nii (distributed with MRIcron).
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Ben Yerys
Sent: Sunday, May 23, 2010 7:54 PM
To: [log in to unmask]
Subject: [FSL] MPRAGE orientation and FNIRT registration problem
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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