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.
|