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 > <[email protected] <mailto:[email protected]>> 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 [email protected] Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
