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Are the streaks the main thing that is bothering you?  It looks like the overall shape might be being corrected.  Is the field map brain extraction good?

Peace,

Matt.

From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Natalia Kowalczyk <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Wednesday, June 1, 2016 at 10:18 AM
To: <[log in to unmask]>
Subject: Re: [FSL] Field Maps FSL

I add also one more image: https://www.dropbox.com/sh/unitz6g8o5fmu16/AACm8jg1V-Xhrn2MOI9qnQj6a?dl=0

2016-05-31 23:07 GMT-07:00 Natalia Kowalczyk <[log in to unmask]>:
Sure.  

1) original DWI image 

2) corrected DWI images -  script: fsl_prepare_fieldmap SIEMENS field_maphase.nii field_map_brain.nii fmap_rads.nii 2.46
Before I used this script I have performed skul stripping (Magnitude image) like: bet filedmap_mag.nii field_map_brain_nii -f 0.3  (with option -f <f> fractional intensity threshold (0->1, value 0.3)
Then I tried to apply Field Map to my DWI images using  script: fugue -i dwi_image01_raw.nii --dwell=0.00082 --loadfmap=fmap_rads.nii --unwarpdir=y- -u resul

3) corrcted using epi_reg- script: epi_reg --epi=dwi_image_raw.nii --t1=struct --t1brain=struct_brain --out=epi2struct --fmap=fmap_rads.nii.gz --fmapmag=fmap_mag fmapmagbrain=fmap_mag_brain --echospacing=0.00082 --pedir=y-

Would be really great if anyone could help me with this.

Thanks in advance!

2016-05-31 21:42 GMT-07:00 Natalia Kowalczyk <[log in to unmask]>:
Sure. 
1) original DWI image 

2) corrected DWI images -  script: fsl_prepare_fieldmap SIEMENS field_maphase.nii field_map_brain.nii fmap_rads.nii 2.46
Before I used this script I have performed skul stripping (Magnitude image) like: bet filedmap_mag.nii field_map_brain_nii -f 0.3  (with option -f <f> fractional intensity threshold (0->1, value 0.3)
Then I tried to apply Field Map to my DWI images using  script: fugue -i dwi_image01_raw.nii --dwell=0.00082 --loadfmap=fmap_rads.nii --unwarpdir=y- -u resul

3) corrcted using epi_reg- script: epi_reg --epi=dwi_image_raw.nii --t1=struct --t1brain=struct_brain --out=epi2struct --fmap=fmap_rads.nii.gz --fmapmag=fmap_mag fmapmagbrain=fmap_mag_brain --echospacing=0.00082 --pedir=y-

Would be really great if anyone could help me with this.

Thanks in advance!

2016-05-31 17:08 GMT-07:00 Matt Glasser <[log in to unmask]>:
Post some before and after images.

Peace,

Matt.

From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Natalia Kowalczyk <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Tuesday, May 31, 2016 at 7:01 PM
To: <[log in to unmask]>
Subject: Re: [FSL] Field Maps FSL

Thanks for your help! 

I have tried with epi_reg :

 epi_reg --epi=dwi_image_raw.nii --t1=struct --t1brain=struct_brain --out=epi2struct --fmap=fmap_rads.nii.gz --fmapmag=fmap_mag fmapmagbrain=fmap_mag_brain --echospacing=0.00082 --pedir=y-

but epi_reg funtion does not improve my DWI data. 

I’m looking forward to hearing other suggetions. 

Bests, 

Natalia 

2016-05-31 14:28 GMT-07:00 Sheena Sharma <[log in to unmask]>:
Hi Natalia,

I have had the same issue and I'm not quite sure the answer but I thought I'd point you to this thread.The thread suggests epi_reg as a better alternative to fugue. However, for me epi_reg gave me worse results then fugue on DWI data, but perhaps I did something wrong. Please let me know how you get on if you try epi_reg. 

Best
Sheena

On Wed, Jun 1, 2016 at 7:27 AM, Natalia K <[log in to unmask]> wrote:
Dear FSL experts,

I would like to correct my orginal DWI data with Field Maps.
I have SIMENS data so I used script: fsl_prepare_fieldmap SIEMENS field_maphase.nii field_map_brain.nii fmap_rads.nii 2.46
Before I used this script I have performed skul stripping (Magnitude image) like: bet filedmap_mag.nii field_map_brain_nii -f 0.3  (with option -f <f> fractional intensity threshold (0->1, value 0.3)
Then I tried to apply Field Map to my DWI images using  script: fugue -i dwi_image01_raw.nii --dwell=0.00082 --loadfmap=fmap_rads.nii --unwarpdir=y- -u result

To conclude the DWI image does not looks better after FM correction. Did I made some mistake during these 3 steps (described above)?

I have also few questions:
1) Should I preprocess the DWI data before applying Field Map? (motion correction etc. using eddy_current)
2) I would like just to apply the FM to the DWI images, other steps I will be doing in other software (preprocessing: resampling, head motion correction etc).
3) Should I use FEAT at FSL to apply FM to DWI images? - I just want to apply the FM to DWI images and all other preprocessing steps I would like to perform in other program.

Any help or ideas would be greatly appreciated!

Thanks so much,

Natalia