Hi Everyone,
I am somewhat new to FSL, having been trained in AFNI. I am working on a Siemens scanner and once I convert the dicom images to nii and check the orientation, my structural and functional are not in the same convention:
fslorient MPRAGE.nii
RADIOLOGICAL
fslorient epi_run1.nii
NEUROLOGICAL
Moreover, the functional data is LPS, not LAS:
mri_info MPRAGE.nii
Orientation : PIL
Primary Slice Direction: sagittal
mri_info epi_run1.nii
Orientation : LPS
Primary Slice Direction: axial
I did not reorient neither data (structural nor functional) before preprocessing my data in FSL as I was advised this was no longer necessary (I was told that FSL is smart enough to figure it out in the spatial registration). However, I am second guessing this information and wanted to be sure. I am particularly worried about registration. I read online:
"FSL templates are LAS and registration in FSL will only do rotations, so starting in LAS orientation will prevent registration errors in the future."
https://wiki.biac.duke.edu/lib/exe/fetch.php?media=biac:fslcourse.pdf
So here is my question: Should I have put my structural AND functional data into LAS format before I preprocessed all my data. If so, is it OK to do it after preprocessing but before spatial registration or should I do it right after nifti conversion? I should note that my registration actually looks fine. I am worried about something more subtle that I cannot detect.
It would be nice if I did not have to re-preprocess from scratch, but I will if needed.
Many thanks,
D
|