Can partial T1 images be segmented?Or, how to get a complete upsampled T1 image after registration?

Dear everyone:
I am reproducing the experimental method for a paper, but I am having a little difficulty. Can you help me? Thank you very much.
My fMRI is tilted and swept (coronal oblique slice orientation) and my procedure is as follows: First, I corrected the BOLD signal for head movement and obtained the mean file(SPM12). Secondly, I upsampled the mean file. Thirdly, I aligned the T1 image to the upsampled mean file and the T1 image would be upsampled indirectly(SPM12). However, the up-sampled T1 image I get is only a part of it and cannot be used for subsequent grey matter and white matter segmentation (which is more accurate after up-sampling)(FSL FAST). Is there any way to be able to upsample the whole T1 when aligning? Or, can part of the T1 be segmented?
Below is my fMRI and registration T1(The whole brain without up-sampling), which you can see is tilted

This is the upsampled T1, containing only the region where the BOLD signal is located