Dr Harms,

We did have moco series. But when processing, we used the original series. From what I understand, this means we are still using the not motion corrected series right?

For practical reasons (we aimed for 2x2x2 and TR=2), we did make some changes to the protocol. We aim to use this for children, so I think motion is something we care a lot about. Multiband has so far generated very good images and localized activations for us. But before we start applying these protocols, would you be so kind to have a look at our parameters?

Thanks

Lingfei Tang

On 18 May 2014 20:00, Lingfei Tang <[log in to unmask]> wrote:

Thanks JA. I added —method=jac and applytopup worked.

I can see now the generated fieldmap did help undistort the BOLD image. The "skull" looks more round and the brain did not stretch as much in the A-P direction. But activation wise (we had a functional localizer and memory task) the two images were more or less the same. Is this expected?

Andreas, you are right that we set the paradigm length to 15. We will reduce it next time we test the sequence. I am not very clear though what this paradigm length mean. Could you clarify?

Lingfei Tang

On 18 May 2014 11:09, Andreas Bartsch <[log in to unmask]> wrote:

Hi,

this sounds like you may have specified a paradigm length of 15 volumes in the BOLD card which prevents you from recording less volumes than that.

Cheers,

Andreas

Von: "Harms, Michael" <[log in to unmask]>
Antworten an: FSL - FMRIB's Software Library <[log in to unmask]>
Datum: Sonntag, 18. Mai 2014 13:14
An: <[log in to unmask]>
Betreff: Re: [FSL] About Topup and Multiband EPI FieldMap

You should be able to collect a single SE-EPI volume for each PE polarity. If not, that sounds like a bug in the Verio implementation. There is a link for report in bugs here:

http://www.cmrr.umn.edu/multiband/

FYI: In the HCP, we collect 3 SE-EPI volumes for each PE polarity.

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: Jesper Andersson <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Sunday, May 18, 2014 3:21 AM
To: FSL - FMRIB's Software Library <[log in to unmask]>
Subject: Re: [FSL] About Topup and Multiband EPI FieldMap

Dear LT,

you need to add —method=jac to your command. The LSR method (which is the default) assumes that you have both blip-directions.

Jesper

On 17 May 2014, at 21:48, Lingfei Tang <[log in to unmask]> wrote:

Thanks Dr. Harms for the prompt reply.
We indeed collected the BOLD multiband sequence in one direction and two short SE-EPI sequences (although for our Simens Verio system we could not figure out how to reduce the number of measurements to less than 15, so we end up having to collect 15 pairs. Is this the limit of the system itself?)

I have generated the field map based on 2 of the 15 pairs of SE-EP with 'topup' and it looks correct. But when I use 'applytopup' I encountered an error.

Since I only have BOLD sequence of one direction, the command I typed is:

applytopup --imain=../MULTIBAND_PPA_12/s012a001.nii --datain=acqparams_pair2.txt --inindex=1 --topup=my_output_pair2 --out=s012a001_corr.nii

In --imain I put the BOLD for one task, and --datain I put the same parameter files as when I ran the 'topup':

0 1 0 .0361

0 1 0 .0361

0 -1 0 .0361

0 -1 0 .0361

and in --topup, it is the output generated by the 2 pairs (coefficient file and field map)

But it gave me an error,

libc++abi.dylib: terminate called throwing an exception

Abort trap: 6

But I have tried to use the following command to correct the 15 pairs based on the same field map/parameter and it worked

applytopup --imain=./cmrrmbep2dses002a001.nii,./cmrrmbep2dses007a001.nii --datain=acqparams_pair2.txt --inindex=1,3 --topup=my_output_pair2 --out=cmrrmbep2dsess_corr.nii

I wonder what I have done wrong.

Thanks

LT

Lingfei Tang

On 16 May 2014 14:48, Harms, Michael <[log in to unmask]> wrote:

Hi,
We collect short two short SE-EPI scans (each only ~ 30 sec) with opposing
polarity. Those are used to derive a fieldmap, which is then used to
correct the GE BOLD scans. The collection of pairs of GE BOLD scans with
opposing phase-encode polarity was done so that we wouldn't introduce an
overall L/R asymmetry in terms of distortion/signal dropout, not because
that was necessary for distortion correction.

In your case, you'll probably want to collect your BOLD with either A>>P
or P>>A phase encoding, and then collect the two short SE-EPI scans with
A>>P and P>>A phase encoding. Then use 'topup' to derive the fieldmap
from those.

Note that it is just as effective to correct the BOLD using a traditional
GE fieldmap acquisition, if you want to go with that approach instead.
(It just takes a little longer to collect -- approx 2 min).

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]

On 5/16/14 1:22 PM, "SUBSCRIBE SPM Lingfei Tang" <[log in to unmask]>
wrote:

>Hi All,
>
>We are trying to acquire data with multiband sequences according to the
>Human Connectom Project
>(http://humanconnectome.org/documentation/data-release/Q2_Release_Appendix
>_I.pdf pg. 38 on) and we would like to correct for the EPI distortions by
>using two dummy EPI sequences (by inverting RO/PE polarity option) and
>the "topup" function suggested by the HCP.
>
>But for our task-related functional data, we can only acquire in one
>direction as the design is event related. In our case, I could generate
>the field map based on the opposing EPI sequences before, but can't use
>applytopup for our real data collected in one direction.
>
>I would like to ask if there is a way still to use Topup to correct the
>distortion or should we collect some other kind of field map to achieve
>this purpose?
>
>Thanks
>LT

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