Hi Sally,
There are a number of ways to do what you want. What will be needed in all cases is a transformation between structural and standard space, the most basic call to do this would be something like:
flirt -in myStructuralImage -ref myStandardSpaceImage -omat struct2standard.mat
you could then use this to transform the output from the epi_reg call to standard space
flirt -in epi2struc.nii.gz -ref myStandardSpaceImage -out epi2standard -applyxtm -init struct2standard.mat
It is also possible to combine the epi_reg warps and the standard space affine transform to avoid multiple interpolation steps.
Hope this helps,
Kind Regards
Matthew
> Hi experts,
>
> I am working with EPI resting-state fMRI data and I have fieldmaps so I would like to perform distortion correction, however, when I try to use applywarp to register the image to standard space the image is clipped and incorrect (please see the attached image)
>
> Can you please have a look at my steps and see if I have missed something or if I am doing something incorrectly.
>
> Cheers,
> Sally
>
>
> The steps that I have followed are:
>
> 1. fsl_prepare_fieldmap with all required data to get outputs (all working well)
>
> 2. run epi_reg on my EPI image (my rsfMRI data), as below
>
> epi_reg --epi=ep2d_3_3iso_Resting.nii --t1=t1.nii.gz --t1brain=bet_brain.nii.gz --fmap=fieldmap.nii.gz --fmapmag=fieldmap_mag.nii --fmapmagbrain=fieldmap_mag_BET.nii.gz --echospacing=0.00035 --pedir=-y --out=epi2struc
>
> 3. invwarp
>
> invwarp -w epi2struc_warp.nii.gz -o test_warp -r ep2d_3_3iso_Resting.nii
>
> 4. applywarp
>
> applywarp --in=epi2struc.nii.gz --ref=/usr/local/fsl/data/standard/MNI152_T1_2mm_brain --out=warped_functional_distortcorrect --warp=test_warp.nii.gz --premat=epi2struc.mat
> (output from this step is attached)
> <Screen Shot 2017-03-11 at 3.27.04 PM.png>
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