As far as the orientation goes, mri_convert will assume that the spm .mat file uses an RAS geometry. You should look at the volume in tkmedit and go through each orientation to make sure that each looks correct. ie, for sag the nose should be to the right, for ax the nose should be at the top. For left/right, tkmedit displays in radiological convention, so make sure your fiducial is on the correct side.

doug

---------- Forwarded message ---------- Date: Wed, 7 Jun 2006 16:02:06 +0100 From: Joao Pereira jmsp2@wbic.cam.ac.uk To: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Segmentation optimization

Here are the acquisistion parameters and some other data as well (images acquired with 1.5T field):

Coronal 3D FSPGR IR GENESIS_SIGNA Sequence: GR Seq Variant: SS\SP\SK Flip Angle: 20 Options: FAST_GEMS\VB_GEMS\EDR_GEMS\PFF TR = 13.9 TI = 650 TE = 4.2 NEX = 1 pixel bandwidth = 81.4 Acq. Matrix = 0\256\224\0 Spatial Resolution = 0.982143 220mmx220mmx174mm (256x256x116) voxel size: 0.86x0.86x1.50mm^3 1.164 pixels per mm

Also, another question that need to check: I transform the Analyze images so that they are SPM oriented (RAS). When I the convert them with mri_convert (no other options set), this orientation (neurological) is maintained, right? (At least it seems so, from the ijk matrix). Please let me know if this interpretation is correct.

Once more, thank you!

Joao

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu]On Behalf Of Bruce Fischl Sent: 06 June 2006 17:50 To: Joao Pereira Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Segmentation optimization

what is the resolution of your images? You might as well send us the complete set of acquisition parameters. Bruce

On Tue, 6 Jun 2006, Joao Pereira wrote:

Hello again,

I've been having some problems with FS segmentation, especially around the temporal lobes, where there is a clear underestimation of the pial surface (and manual edits are not being too successful). The problem is clearly related to the poor resolution of the used images.

Are there any parameters to change in order to optimise the segmentation process?

Also, in order to evaluate the segmentation I want to use the grey matter segmented volume mask. Is it the ?h.ribbon.mgz files or should I consider something else?

Thank you again.

Joao Pereira

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