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Hi Sally,

I'm not an expert myself but I use just one 3D image as input to  
epi_reg, for example,

   epi_reg --epi=func_meanvol ... --out=epi2struct

Then, you can combine epi2struct_warp with the struct2standard warp  
(previously computed with flirt/fnirt) using convertwarp.

After that, I also combine this with each volume's transformation from  
mcflirt so that I can use applywarp to warp each volume of the time  
series directly to standard space with one transformation.

You could also take a look at the relevant scripts in the HCP  
pipelines, where this is being done in a similar way, I believe. I  
don't remember if they use fsl_prepare_fieldmap and epi_reg, though.

Cheers,
Kris


Quoting Sally Grace <[log in to unmask]>:

> Hi experts,
>
> I have previously analysed my EPI resting-state data with the following
> pipeline using command line tools, but I would like to add distortion
> correction and I am unsure at what stage to perform slice timer, motion
> correction (mcflirt), and distortion correction.
>
> *Old pipeline:*
>
>    1. STRUCTURAL PREPROCESSING (Input is T1 image)
>       1. fslreorient2std
>       2. BET brain extraction on T1's
>       3. FLIRT (register T1 to standard space and generate and affine)
>       4. FNIRT (coregister T1 native to standard space)
>    2. FUNCTIONAL PREPROCESSING (input is resting-state EPI)
>       1. fslreorient2std
>       2. slicetimer
>       3. mcflirt
>       4. fslmaths -Tmean to get a merged and average .nii using the mean
>       across time
>    3. functional FLIRT (-in = is fslmaths'd output, -ref = bet'd T1)
>    4. applywarp based on native T1 (--in= mcflirt'd functional --premat =
>    affine from flirt)
>
>
> My question is, at what stage in the above pipeline could I perform
> distortion correction? Below are my steps to perform distortion correcton
> which works well. However, I would like to also perform slice timer and
> motion correction so I have attempted to input the mcflirt'd output into
> epi_reg but that does not work.
>
>    1. *fsl_prepare_fieldmap*
>    2. *epi_reg: *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. *structural flirt:* flirt -in myStructuralImage -ref
>    myStandardSpaceImage -omat struct2standard.mat
>    4. *functional flirt:*  flirt -in epi2struc.nii.gz -ref
>    myStandardSpaceImage -out epi2standard -applyxfm -init struct2standard.mat
>
> Any help is greatly appreciated. Thank you!
>
> Kind regards,
> Sally.