Hello,
Are your PD images already in the same space as your T1 images?
Kind Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
> On 2 Oct 2017, at 17:15, Ibrahim Malik <[log in to unmask]> wrote:
>
> Hi Jesper, thank you for the reply. Here are the commands that I have been using:
>
> # (1) First I performed a linear registration using flirt:
>
> Flirt -ref MNI152_T1_1mm_brain -in T1.nii.gz -dof 12 -cost normcorr -searchcost normcorr -omat T1_in_MNI.mat
> flirt -ref MNI_1mm_brain -in T1.nii.gz -applyxfm -init T1_in_MNI.mat -out T1_in_MNI.nii.gz
>
>
> # (2) Non_Linear Registration
> #Roi_in_native a PD images subsample to T1 resolution
>
> fnirt --in=T1.nii.gz --aff=T1_in_MNI.mat --ref=MNI152_T1_1mm_brain.nii.gz --refmask=MNI152_T1_1mm_brain_mask_dil.nii.gz --cout=my_non_linear_transf --config=T1_2_MNI152_2mm
>
> applywarp --ref=MNI152_T1_1mm_brain.nii.gz --in=T1.nii.gz --warp=my_non_linear_transf --out=my_warped_struct
>
> #(3) Applying the warp to my ROI. The ROIs were drawn on a Proton density images
>
> applywarp --ref=MNI152_T1_1mm_brain.nii.gz --in=ROI.nii.gz --warp=my_non_linear_transf --out=my_warped_ROI
>
>
> Thank you, Jesper.
>
> Ibrahim
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