Hi Jesper

Thank for your help! This is the coman I used:

fugue -v -i epi_ecc --icorr --unwarpdir=y- --dwell=0.00073 --loadfmap=fieldmap_s4_2_nodif_brain -u epi_ecc_epic

As you can see, I was using the flag you mentioned. I've tryed without the flag and it works. I guess the signal dropout was due to missalignment.

Just for the record (this post could help somebody), here are links to fslview's screenshots form FA images. As you can see there is a literally hole on it.

org: https://drive.google.com/file/d/0BxzotkTPKUQQMWxtM1NIbjZQbjQ/view?usp=sharing

usign --icorr flag: https://drive.google.com/file/d/0BxzotkTPKUQQVmk2aU5leTRHRlE/view?usp=sharing

not usign --icorr flag: https://drive.google.com/file/d/0BxzotkTPKUQQZEhKMUhaWFRQcGc/view?usp=sharing

Thsnks again,
Cheers

2017-03-25 9:54 GMT-03:00 Jesper Andersson <[log in to unmask]>:
Hi again,

I've gotten some diffusion data and I want to correct EPI ditortion on them. I've got fieldmap from the SIEMENS scans.

 sorry, I just now saw that this was diffusion data, so yes, SE-EPI.

Jesper


I've found an exelente example pipeline on the forum which take in acount the registration beetwen the fildmap and epi image (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1606&L=fsl&P=R103508&1=fsl&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4).

This pipeline work fine, but my results have a "hole" in the brain base (near to stem). I think it is because of the shift in the correction. I wonder if this hole is due to signal loss?

The rest of the volume seems fine, but I am worried about this hole could disturb next steps (fiting model anda tracking).

Here are three links to screenshots from fslview which you can see the hole.

original: https://drive.google.com/file/d/0BxzotkTPKUQQdE5JRUczUm9zTUE/view?usp=sharing

original to corrected: https://drive.google.com/file/d/0BxzotkTPKUQQakJwOGtKM2w0aTQ/view?usp=sharing

corrected: https://drive.google.com/file/d/0BxzotkTPKUQQa0Z2dGhubG9Jbms/view?usp=sharing

Being all for now, I await a reply

--
Bioing. Guido Pascariello
Becario Doctoral CIFASIS - CONICET
Grupo de Procesamiento de Señales Multimediales
Tel/Fax: 54 341 482 6300/ 1771/ 72 Int. 386




--
Bioing. Guido Pascariello
Becario Doctoral CIFASIS - CONICET
Grupo de Procesamiento de Señales Multimediales
http://www.cifasis-conicet.gov.ar/
Tel/Fax: 54 341 482 6300/ 1771/ 72 Int. 386