Dear Jian,

I have question about --datain calculation.

In the TOPUP wiki it says:
"...you have opted for partial k-space (in order to reduce the echo time), collecting only 64 echoes. In this case the level of distortion will be identical to what it would have been had you collected all 96 echoes, and you should put 0.095 in the fourth column."

Is this only valid for one coil case?

We use GRAPPA with Accel. factor =2 , my UpBilp echo spacing = 0.57ms and DownBilp echo spacing =0.7ms with 98*98 matrix.

your total readout time (which should be given in seconds) will be

Up: (98/2 - 1)*0.00057 = 0.027 sec

Down: (98/2 - 1)*0.0007 = 0.034 sec

Topup is designed to be able to handle cases like these, i.e. where you have different readout times, but I must admit I haven't tested it much lately. I would be quite interested to have a look at the b0s from you data just to see how well it does.

Good luck Jesper

How do I calculate readout times in my case?

Thanks in advance for the help.

Jian

Date: Thu, 11 Oct 2012 13:31:03 +0100
From: [log in to unmask]
Subject: Re: [FSL] Topup phase-encode question
To: [log in to unmask]

Hi Joanne,

and relevant also for Ben Jeurissen and Richard Nibbs that reported the same problem.

The bug has been identified and fixed. The fix will be part of FSL 5.0.2, which will be announced on the mailbase.

Jesper

On 10 Oct 2012, at 21:44, Joanne Lin wrote:

Hi Jesper,

Thank you again again for taking a look at my data!

The reference number is 694787 - I included the b0 images, the data acquisition parameters and the b02b0.cnf file (though this is the one that it came with).

Many thanks,
Jo
From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Jesper Andersson [[log in to unmask]]
Sent: Tuesday, 9 October 2012 10:05 p.m.
To: [log in to unmask]
Subject: Re: [FSL] Topup phase-encode question

Hi Joanne,

this sounds like a similar problem to what someone else recently reported. I haven't been able to replicate it using my own data so it would be helpful if you could upload yours to see if I can work out what is wrong.

Jesper

On 9 Oct 2012, at 02:55, Joanne Lin wrote:

Hi everyone,

Apologies about asking yet another question about topup but I am having some trouble with a particular dataset.

I have a set of b0 images acquired AP, which is cool but the radiographers accidentally acquired my second set of b0 images in the LR direction (usually it’s PA).

Similarly to the wiki example, I processed it as normal except I specified my phase-encoding directions like this –

0 -1 0 1 (for AP b0 images)
1 0 0 1 (for LR b0 images)

I got the message –
Image Exception : #3 :: Attempted to add images/ROIs of different sizes
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted

I thought the images were the same size but was there something different about the LR images or something I should have done before using them?

Thanks heaps!

Cheers,
Jo