No, I'm saying that it is my current understanding that the meaning of a "1 0 0" vector is *dependent* on the image orientation -- i.e., "1 0 0" would have a different meaning for a LAS oriented volume vs. an RAS oriented volume.  MJ or Jesper can hopefully confirm.

There are many stages of the acquisition/recon chain where the sign can get swapped relative to what you might expect, which is why it is always a good idea to purposely invert the direction of the correction relative to what you think is right, and see if the data actually gets worse.

cheers,

-MH

-- 

Michael Harms, Ph.D.

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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]&cc=&bcc=&su=&body=','_blank');return false;">[log in to unmask]

From: Chris Filo Gorgolewski <[log in to unmask]&cc=&bcc=&su=&body=','_blank');return false;">[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]&cc=&bcc=&su=&body=','_blank');return false;">[log in to unmask]>
Date: Thursday, December 3, 2015 11:35 AM
To: FSL - FMRIB's Software Library <[log in to unmask]&cc=&bcc=&su=&body=','_blank');return false;">[log in to unmask]>
Subject: Re: [FSL] Describing phase encoding direction in topup

Hi,

Thanks for your reply. So you are saying that topup expects "1 0 0" vector for R >> L sequences independent of the image orientation (LAS, RAS, ALS...)?

Is this the same with the --unwarpdir in fugue?

Best,

Chris

On Wed, Dec 2, 2015 at 5:59 PM, Harms, Michael <[log in to unmask]&cc=&bcc=&su=&body=','_blank');return false;">[log in to unmask]> wrote:

Hi,

I believe it depends on the orientation of your NIFTI file.  If you have an LAS oriented volume, then there is no inconsistency relative to TOPUP/Faq examples -- i.e., P>>A and R>>L are both in the direction of increasing index.

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]&cc=&bcc=&su=&body=','_blank');return false;"> [log in to unmask]

From: Chris Filo Gorgolewski <[log in to unmask]&cc=&bcc=&su=&body=','_blank');return false;">[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]&cc=&bcc=&su=&body=','_blank');return false;">[log in to unmask]>
Date: Wednesday, December 2, 2015 6:53 PM
To: FSL - FMRIB's Software Library <[log in to unmask]&cc=&bcc=&su=&body=','_blank');return false;">[log in to unmask]>
Subject: [FSL] Describing phase encoding direction in topup

Dear all,

I was trying to translate a the phase encoding vectors used in TOPUP from the usual LR/RL, AP/PA to something more scanning object agnostic (afterall I can run topup n a scan of a watermelon that does not have left/right, anterior/posterior sides). From what I see in http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TOPUP/Faq there is some inconsistency.

For the second axis (y) if the phase encoding direction goes from zero to maximum index the vector in --datain should be set to 0 1 0 (equivalent to P >> A). If if the direction goes from maximum index to zero it should be set to 0 -1 0. (equivalent to A >> P) This makes sense.

However for the first axis (x) the situation is opposite. if the phase encoding direction goes from zero to maximum index the vector in --datain should be set to -1 0 0 (equivalent to L >> R). If if the direction goes from maximum index to zero it should be set to 1 0 0 (equivalent to R >> L).

Am I correct in my deductions? Is there a reason for this inconsistency?

Best,

Chris Gorgolewski

 

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