Hi Derya,
If you have already run feat pre-processing ( which appears to be the case from the folder names ) and the structural image you want to register to is the same as the one in the script ( sub-11A_T1w.nii.gz ) then the transforms needed will have already been generated in the <blah>.feat/reg directory.and you can proceed to the applywarp step described below.
If however, you are looking to register the pre-processed functional data to a _different_ structural image ( of the same subject obviously! ) then the best approach is to run epi_reg with the corresponding example_func.nii.gz as input. However the transforms are generated you can then use them with applywarp to create the structural-space version of the functional data. To transform the structural image to functional space ( if this is needed for some reason ) you can use applywarp again, but with the inverse transform.
Hope this helps,
Kind Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
> On 14 Aug 2022, at 23:48, Derya Adil <[log in to unmask]> wrote:
>
> Hi there,
>
> I would really appreciate your help.
>
> Do I need any previously made files in order to run the argument to register the participants functional scan to the anatomical scan?
>
> I already created the skull stripped file and a str2standard.mat file.
>
> I made these two arguments as you see below, and both give me a warning….I am not sure if FSL changed their tools or if I need to create a document before doing this registration. The functional file is in 4D, so I am not sure what is the issue…
>
> Warning: An input intended to be a single 3D volume has multiple timepoints. Input will be truncated to the first volume, but this functionality is deprecated and will be removed in a future release.
>
> Scripts I modified:
>
> Register.sh
>
> echo '........... now running FLIRT ........... '
> epi_reg --epi=/mnt/c/Users/Brain/Desktop/11A/preprocess.feat/filtered_func_data.nii.gz --t1=/mnt/c/Users/Brain/Desktop/11A/subject11A/anat/sub-11A_T1w.nii.gz --t1brain=/mnt/c/Users/Brain/Desktop/11A/subject11A/anat/sub-11A_T1w_brain.nii.gz --out=epi2struc.nii.gz
> done
>
> struc2epi.sh
>
> echo
>
> #register T1 to EPI space
> flirt -in /mnt/c/users/Brain/Desktop/11A/subject11A/anat/T1.nii.gz -ref /mnt/c/users/Brain/Desktop/11A/preprocess.feat/filtered_func_data.nii.gz -out /mnt/c/users/Brain/Desktop/11A/derivatives/reg/11A_str2epi -init /mnt/c/users/Brain/Desktop/11A/derivatives/reg/str2epi.mat -applyxfm
> done
>
> Any advice or guidance would be amazing… I have been stuck on this for about a week now! I notice that a lot of the examples online use the argument with “example_func” but this is in 3D, and I wanted to register to the actual preprocessed functional scan. (I could be misunderstanding here).
>
> Thank you in advance,
>
> Derya
>
>
>
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