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If the labels correctly describe the anatomy in ‘fslview’, then just use ‘fslreorient2std’.

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: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Rosalia Dacosta Aguayo <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Wednesday, August 17, 2016 at 9:49 AM
To: FSL - FMRIB's Software Library <[log in to unmask]>
Subject: [FSL] Choosing reorientation of some images

Dear FSL experts,

I have doubts regarding reorienting some of my images.

I have been looking at fsl mailing list archives: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1310&L=FSL&P=R41895&1=FSL&9=A&

And I have followed the instruccions in the link adviced by Mark Jenkinson in this email:    https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Orientation%20Explained

I have been looking every step:

1. Labels are not missing or wrong: ok, when I oppen my problematic images I can see that labels in FSLView appears...as I have used dcm2nii to convert dicom to nifti I can guess that labels are not wrong...ok because it is a very good tool (Chris Rorden).

2. The labels in FSLView are correct but the image is wrongly oriented....well, I have compared lables in FSLView with a good oriented image with the one I have problems, and I have seen that labels are changed...and I guess that this is because the image is oriented in a different way that MNI template (i.e.: in the coronal view, I can see that S, I and R, L are just inverted...: where it should be R now is L and the same for the other two lables).

The question here is that I am not sure if I should combine fslorient and fslswadim in conjuntion....or just fslreorient2std (that is the choice I would make here...).

Here it is the link to a folder created in my dropbox just for this issue in order you can evaluate better the situation, not only the description. I have just sent and email to share this link with FSL...I hope this works...if there is another way of doing this, please, do not hesitate to tell me.

But I am unsure and I would greatly appreciate any help in this issue, so I can learn how to cope with this problem in the future.

With my kind regards,

Rosalia




--
Rosalía Dacosta-Aguayo, Post-Doctoral Researcher.
Biomedicine, PhD
Clinical Neuropsychologist

Department of Neurosciences.
Group of Neurodegenerative Diseases
Gaixotasun Neuroendekapenezko Taldea
Neurozientziak Arloa

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