Hi Doug,
I realize now that I was unclear of the function of kvlQuantifyHippocampalSubfieldSegmentations.sh
It creates a summary file of volumes for the left and right subfields as volumeStats_X.txt (where x is left or right). It writes the files into the mri subdirectory. Is there a scripted way to combine these stat files into a table format for a group?
Thank you for all your help.
Sal
On Tue, Aug 6, 2013 at 12:17 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
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 greve@nmr.mgh.harvard.edu>> wrote:
mri/hippsubfieldseg.mgzThank 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 Phone Number: 617-724-2358 Fax: 617-726-7422
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