2013/7/3 Harms, Michael <[log in to unmask]>

The RL PA IS options in 'fslswapdim' will not fix the labels if they are originally incorrect. And the anatomical labels approach is not an option if the q/sform is not defined.

See

http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Fslutils

and

http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Orientation%20Explained

for the detailed, official FSL explanation of all this.

The key issue is how are you going to know that you have R/L correctly defined unless a marker of some sort was attached as part of the acquisition?

Your best bet, if at all possible, is to go back to the original DICOMs and convert to NIFTI from those.

cheers,

-MH

--

Michael Harms, Ph.D.

-----------------------------------------------------------

Conte Center for the Neuroscience of Mental Disorders

Washington University School of Medicine

Department of Psychiatry, Box 8134

660 South Euclid Ave. Tel: 314-747-6173

St. Louis, MO 63110 Email: [log in to unmask]

From: Rosalia Dacosta Aguayo <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Wednesday, July 3, 2013 10:33 AM
To: FSL - FMRIB's Software Library <[log in to unmask]>
Subject: Re: [FSL] fslswapdim

Hi Erica,

Your images are in nifti format...right?

If so, you do not have to use {'z -x y', '-x y z'}...you can use RL PA IS...or other combinations depending on how you want your images and how they appear actually.

So, for example, you can try:

fslswapdim t1.nii.gz RL PA IS nt1.nii.gz

Hope this helps,
Rosalia.

2013/7/3 Erica Tatham <[log in to unmask]>

Hello Lovely Helpers at FSL,

My question is regarding fslswapdim.
In my dataset I have 3 participants where the slicing in FSL needs to be changed. Therefore,
… my coronal slice is in the place the sagittal slice
… my sagittal slice is in the place of the axial slice
… my axial slice is in the place of the coronal slice
and additionally, my coronal slice is turned 90 degree angle.
[image attached for reference]

The unfortunate thing is that these are analyze files and therefore do not have a co-ordinate system attached to them. On the positive side, my team has determined that when the slices are in their ‘normal’ position, then they follow the standard coordinate system.

My question is this: is there anyway to move around my images (and rotate the one coronal slice), as they need to be re-ordered before being processed. Following the re-ordering I would then set my s/q-form to standard.
[the reverse of this question can also be considered… setting the s/q form and then moving around the images while not changing the label].

I found the following command through another person’s website, but it doesn’t seem to be right/work:
fslswapdim t1.nii.gz {'z -x y', '-x y z'} t1testswap.nii.gz

I read that this can be very very tricky, so I wanted another opinion.

Thank you very much,
Erica Tatham

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