In general, the software packages don't really care how the data were acquired (though FSL generally wants images that are in radiological convention -- check their web site). You do want to make sure that all your subjects were acquired in the same way (ie, don't acquire some subjects axially and some subjects sagittally). If you do have a mixture, try to make sure that your groups are balanced. doug

Antonella Kis wrote:

Dear Freesurfers,

I have a set of MRI data collected in an Axial_T1 and some in Sag3D_T1. I wonder if after dcm to nii conversion when I get a 3D or 4D volume (if further use for FSL) it really matter how my data was acquired (Axial or Sag) since the NIFTI file is in fact a volume. Should I do a conversion for all the files in Axial or Sag? I am planning to use this data in Qdec and also in FSL to do some DTI studies, so I will need to register this data into MNI space. Also, how I can cut from the nii file's slices in order to bring two files to the same dimensions (x, Y, Z)?

Many thanks, Antonella