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Dear Niels,

Thank you very much.

You and Matthew were really helpful.

All the best,

Kostakis

---
Electrical and Computer Engineer
Phd Candidate in Brain Imaging
Medical Image Processing, Algorithms and Applications
National Technical University of Athens
9,Iroon Polytechneiou str.,
157 73 Zografou Campus,
Athens, GREECE
phone:+30 210 772 3577


On 06/11/2018 15:17, Niels Bergsland wrote:

Hi Kostakis,
Yes - this is the normal behavior from the Siemens gre_field_mapping sequence. The phase image is the difference image whereas the two magnitudes correspond to those obtained from the first and second echo. You can use either one, or calculate the average and use the resulting image for subsequent processing.
 
-Niels

On Tue, Nov 6, 2018 at 2:08 PM Kostakis Gkiatis <[log in to unmask]> wrote:

Dear Matthew,

Thanks for the reply.

After a bit of research, I found that during the acquisition it produces two magnitude images, one for each TE, and one phase image.

The data was acquired on a Siemens Avanto Fit 1.5T scanner with software syngo MR E11.

Can you verify that this behavior is normal?

Is it ok if I choose one of the two images and continue the analyses normally?

Thank you in advance,

Kostakis

---
Electrical and Computer Engineer
Phd Candidate in Brain Imaging
Medical Image Processing, Algorithms and Applications
National Technical University of Athens
9,Iroon Polytechneiou str.,
157 73 Zografou Campus,
Athens, GREECE
phone:+30 210 772 3577


On 02/11/2018 17:54, Matthew Webster wrote:

Hello,
  The old version of FSL would only read the first volume of the fieldmap ( it would effectively ignore the second ). The new version of FSL is specifically expecting a single 3D volume and will generate an error if the fieldmap is 4D.
 
Hope this helps,
Kind Regards
Matthew  
--------------------------------
Dr Matthew Webster
FMRIB Centre 
John Radcliffe Hospital
University of Oxford

On 2 Nov 2018, at 11:10, Kostakis Gkiatis <[log in to unmask]> wrote:

Hello,

You are correct. Fieldmap has two volumes, I'm so sorry I haven't seen it.

I just noticed that while the phase image has one volume, the magnitude image that I input into Fsl_prepare_fieldmap has two volumes slightly different. This image is the raw image after the nifti transformation that I did with MRICron. Is this normal? Is it ok if I just take one of them and proceed the analysis?

Now I am confused why the old version of FSL was working..

Any insight would be helpful.

Thank you in advance,

Kostakis

---
Electrical and Computer Engineer
Phd Candidate in Brain Imaging
Medical Image Processing, Algorithms and Applications
National Technical University of Athens
9,Iroon Polytechneiou str.,
157 73 Zografou Campus,
Athens, GREECE
phone:+30 210 772 3577


On 02/11/2018 12:53, Matthew Webster wrote:

Hi,
     Can you confirm that the input fieldmap ( selected via the GUI ) only has 1 volume?
 
Kind Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre 
John Radcliffe Hospital
University of Oxford

On 1 Nov 2018, at 13:14, Gkiatis Kostakis <[log in to unmask]> wrote:

Dear FSL experts,

I recently upgraded to FSL 6.0 and I run some test just to verify everything looks good.
When I tried to run Melodic with the option of B0 unwarping with the exact same input as in the old version of FSL, I get this error when fugue is running:

/usr/local/fsl/bin/fugue --loadfmap=FM_UD_fmap --savefmap=FM_UD_fmap_tmp_fmapfilt --mask=FM_UD_fmap_mag_brain_mask --despike --despikethreshold=2.1
Image Exception : #75 :: 3D only method called by higher-dimensional volume.
terminate called after throwing an instance of 'armawrap::AWException'
 what():  3D only method called by higher-dimensional volume.
Aborted

After a bit of debugging, I noticed that both images, FM_UD_fmap and FM_UD_fmap_mag_brain_mask, as well as FM_UD_fmap_mag_brain and FM_UD_fmap_mag have 2 volumes per image, the one that I gave as input and the one that was created from the script. I am not even sure how this is possible. Instead of replacing the images, the script created a 4th dimension and saved images there.

I tried to run Feat as well and got the same error. I got no errors when I run without B0 unwarping option.

Am I doing something wrong?
How can I fix this?

Thank you in advance.
Gkiatis Kostakis

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--
Niels Bergsland
Integration Director / Research Assistant Professor of Neurology
Buffalo Neuroimaging Analysis Center / University at Buffalo
100 High St. Buffalo NY 14203
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