[Freesurfer] spgr orientation and re-slicing

2011-12-14 Thread Cat Chong
Dear Experts, I am sorry for the basic question but we have a dataset of subjects we  like to analyze for which  we have different slice thicknesses and orientations in dicom format. All T1's  collected were SPGR volumes with the same scanner parameters. My question was: Do you advice to re-ori

Re: [Freesurfer] spgr orientation and re-slicing

2011-12-14 Thread Douglas Greve
Hi Catherine, no, don't do anything to your data, just run it as it is through recon-all. Also, it is not so good to have different acquisitions in your study (though it does depend a bit on how different they actually all). You should make sure that your study is balanced across the different

Re: [Freesurfer] spgr orientation and re-slicing

2011-12-14 Thread Bruce Fischl
Hi Catherine, it shouldn't be necessary, but you should be very careful that any effects you find are biological ones and don't simply reflect acquisition differences. cheers Bruce On Wed, 14 Dec 2011, Cat Chong wrote: Dear Experts, I am sorry for the basic question but we have a dataset o