Hello: I have big file of pts with medial temporal lobe epilepsy (they usually have hippocampal sclerosis, atrophy; sometimes MRI signal changes in amygdala). Pts are scanned with 'oblique' sequence, as it is perpendicular to long axis of hippocampus. Can these oblique sequences be used for FreeSurfer cortical reconstruction and subcort. volumes? I put some of them through 'recon-all' pipeline, which finished 'without errors'. In the 'stats' files (aseg.stats) of those subjects, I am missing volumetric values for left hippocampus and left amygdala. Patients are before surgery, so they have left structures for sure (even original dicom data are complete). The right hipo and amygdala volumes are stated in mm3 as expected. Why is that? Thanks for the advice.
Oblique should not be a problem. What is your voxel size? doug
On 09/14/2012 02:08 PM, Zuzana Nedelska wrote:
Hello: I have big file of pts with medial temporal lobe epilepsy (they usually have hippocampal sclerosis, atrophy; sometimes MRI signal changes in amygdala). Pts are scanned with 'oblique' sequence, as it is perpendicular to long axis of hippocampus. Can these oblique sequences be used for FreeSurfer cortical reconstruction and subcort. volumes? I put some of them through 'recon-all' pipeline, which finished 'without errors'. In the 'stats' files (aseg.stats) of those subjects, I am missing volumetric values for left hippocampus and left amygdala. Patients are before surgery, so they have left structures for sure (even original dicom data are complete). The right hipo and amygdala volumes are stated in mm3 as expected. Why is that? Thanks for the advice.
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Hi Zuzana
I don't think we can diagnose it without seeing some images. The obliques should be ok, as long as they are whole brain and reasonably high resolution and good T1-weighted contrast.
cheers Bruce On Fri, 14 Sep 2012, Zuzana Nedelska wrote:
Hello: I have big file of pts with medial temporal lobe epilepsy (they usually have hippocampal sclerosis, atrophy; sometimes MRI signal changes in amygdala).Pts are scanned with 'oblique' sequence, as it is perpendicular to long axis of hippocampus. Can these oblique sequences be used for FreeSurfer cortical reconstruction and subcort. volumes? I put some of them through 'recon-all' pipeline, which finished 'without errors'. In the 'stats' files (aseg.stats) of those subjects, I am missing volumetric values for left hippocampus and left amygdala. Patients are before surgery, so they have left structures for sure (even original dicom data are complete). The right hipo and amygdala volumes are stated in mm3 as expected. Why is that? Thanks for the advice.
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas N Greve -
Zuzana Nedelska