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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. > Images are here: > https://www.dropbox.com/home/DWI%20images%20and%20Field%20Maps > > 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. >>> >>> Iım 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 >>>> <https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;5b5357c1.1507> .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 >>>> >>> >> >