How to deal with multiple sessions in sct_fmri_moco?

This is a continuation of the post started on Sourceforge.

Hi Alexandra,

When comparing the SPM and SCT results (using v4.0.0_beta.0), both seem of similar quality. See below an animation that compares SPM, SCT and no-moco.

Results in SCT are definitely better than the ones you obtained on your side. Would you mind trying it again with the following commands and let me know if you obtain the same results as me?

sct_image -i *.nii -concat t -o fmri.nii.gz
sct_maths -i fmri.nii.gz -mean t -o fmri_mean.nii.gz
sct_get_centerline -i fmri_mean.nii.gz -c t2
sct_create_mask -i fmri_mean.nii.gz -p centerline,fmri_mean_centerline.nii.gz -size 65mm -f cylinder -o mask_fmri.nii.gz
sct_fmri_moco -i fmri.nii.gz -m mask_fmri.nii.gz -x spline


Hi Julien,

I now updated the toolbox from version v4.0.0_beta.0 to the latest and ran the code you provided on sourceforge and still I found a difference between your sct_moco_mean and my sct_moco_mean. Now, seeing that here, you added the -x option to your moco, I reran the analysis and now it seems, that our mean images are identical. So, it seems reasonable to me to use spline interpolation in all my future analyses.

I still attach the gif to this post to show the difference between spline and linear interpolation.


Thank you so much for your help!

Here now the gif:

Awesome! I’m glad we figured out that part. Let me know if you still need assistance about the inter-session registration.