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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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