If I use fslchfiletype to convert my nii data to Analyse to do my stats in SPM, when I open the data in SPM, where is the Left? same as FSL and I have to put a - sign to my x coordinates?
Hi Elise. Did you place fiducials on your subjects' foreheads before scanning? This is very important as then you will always know which is left and right.
SPM should read the header file appropriately but you should always check. I would echo Jerome's comment and test this using a scan where you have a forehead marker. If you don't have any scans with a marker, make an edit to one of your own images. For example you could make a circular mask, mask out a hole on the left side of a test image, and then load that up in SPM.
I would also agree with Eugenio that you should just stick with .nii files rather than going to Analyze. fslchfiletype can go from .nii.gz to nii or you can use mri_convert within Freesurfer.