Hello, I am new to fmriprep and have some data preprocessed through the pipeline. (Fmriprep is an excellent resource, btw!)
When I open the preprocessed images
*_preproc.nii.gz as an overlay on the the 2mm MNI brain as provided by fsl on
fslview_deprecated, I am unable to view them. I get an image mismatch warning.
When I run fslhd to look at the header information of
*_preproc.nii.gz, it looks like:
and same with sform
on the MNI brain provided by fsl, the header information looks like:
and same with storm
Looks like the images come right-left flipped out of fmriprep. It seems to me that majority of images have qform/sform as Right-to-Left, so what was fmriprep’s rationale to choose Left-to-Right orientation? Do I need to switch storm and qform to do further analyses, because I can’t use
fslmaths function right now between two images because of this mismatch issue. How do I switch the qform/sform to give a proper orientation? Any help would be appreciated, thanks, I am still learning fmriprep!