oh, sorry, you are right. I had thought that they generated a single file with the segmentations. In this case, you will need to threshold at some value of the posterior probability. Alternatively, you could generate a segmentation file by selecting the seg at a voxel that has the highest post prob using mri_concat with the --max-index-prune option. You'd then create your own LUT and run mri_segstats using the seg volume and the LUT
doug


On 08/06/2013 03:09 PM, Salil Soman wrote:

On Mon, Aug 5, 2013 at 2:22 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

    mri/hippsubfieldseg.mgz


Thank you Doug. Just to clarify the code you suggested earlier, should "mri/hippsubfieldseg.mgz" be replaced with each of the specific hipposubfields:

posterior_Left-Cerebral-Cortex.mgz
posterior_Left-Cerebral-White-Matter.mgz
posterior_Left-Hippocampus.mgz
posterior_Right-Cerebral-Cortex.mgz
posterior_Right-Cerebral-White-Matter.mgz
posterior_Right-Hippocampus.mgz
posterior_left_CA1.mgz
posterior_left_CA2_3.mgz
posterior_left_CA4_DG.mgz
posterior_left_fimbria.mgz
posterior_left_hippocampal_fissure.mgz
posterior_left_presubiculum.mgz
posterior_left_subiculum.mgz
posterior_right_CA1.mgz
posterior_right_CA2_3.mgz
posterior_right_CA4_DG.mgz
posterior_right_fimbria.mgz
posterior_right_hippocampal_fissure.mgz
posterior_right_presubiculum.mgz
posterior_right_subiculum.mgz


If not, I do not see a file called mri/hippsubfieldseg.mgz for my output, and any advice on where I could find it would be great.

Best wishes,

Sal

--
Salil Soman, MD, MS
Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory
Fellow - Palo Alto War Related Illness and Injury Study Center
WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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