Hi Dierdre
not sure a FLAIR with that thick slices will be very useful, but the typical workflow is to run recon-all with the T1, then when it's done you can run recon-all with a special switch to register and use the FLAIR. Note that this is only in 5.2, which isn't quite out yet (although you could get a beta if you want)
cheers Bruce
On Tue, 8 Jan 2013, Deirdre O Shea wrote:
Hi,
I would like to try running recon-all for some subjects using two source images in combination. The first image is a FLAIR with dimensions 288x288x30, while the second is a T1 with dimensions 256x256x165. Furthermore, the each FLAIR voxel has dimensions of 0.79x0.79x4.5 mm, while each T1 voxel has dimensions 1x1x1 mm.
I tried running the following command:
recon-all -i FLAIR/FLAIR_P00004210_S0001.nii -i T1/T1_P00004210_S0001.nii -subjid FreeSurfer_FLAIR
But I got the following error message:
ERROR: inputs have mismatched dimensions!
Is there an inbuilt command in FreeSurfer that will override this error message and perform a linear registration of the two images into the same space automatically, or do I need to perform the registration manually before starting with recon-all?
Thank you, Deirdre