If you want the volume of cortex, you should definitely not use aseg.mgz. aparc+aseg is better, but the best is to use the surface-based measure found in aseg.stats
doug On 04/22/2014 10:55 AM, pfot...@nmr.mgh.harvard.edu wrote: > Hi Doug, > > Thanks again for your reply. One last question: The aseg.mgz file includes > the cortex as well. If I want to extract the cortex from the aseg.mgz > file, should I binarize both the aseg.mgz and aparc_aseg.mgz files and > subtract them, and then use the result in the mri_segstats command, or is > there a different way? > > Thanks, > Panos > >> On 4/18/14 4:25 PM, pfot...@nmr.mgh.harvard.edu wrote: >>> Hi Doug, >>> >>> Thanks for the quick reply! In addition: >>> >>> 1) The average intensity measure in the above example does not include >>> the >>> intensity of the skull, just everything inside, right? >> It includes all the structures that are segmented in seg. If there is >> not a skull segmentation, then it will not be in the output list. >>> 2) Just to be clear on the purpose of including the segmentations in the >>> command line: The segmentations only specify the areas of the brain that >>> you would like to measure the intensity on, but besides that they don't >>> provide any intensity info by themselves, would that be correct? That is >>> the purpose of the --i flag, right? >> Correct >> doug >>> Thanks again for your help, >>> Panos >>> >>>> On 4/18/14 3:32 PM, pfot...@nmr.mgh.harvard.edu wrote: >>>>> Hi FS community, >>>>> >>>>> I had some questions regarding the mri_segstats command: >>>>> >>>>> 1) In the excludeid flag, are the ids the ones shown in the >>>>> FreeSurferColorLUT.txt? >>>> Yes >>>>> 2) In case I would like to measure the mean intensity of the orig file >>>>> as >>>>> outlined in the second example in >>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats: >>>>> >>>>> mri_segstats --seg $SUBJECTS_DIR/bert/mri/aseg >>>>> --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt >>>>> --nonempty --excludeid 0 --sum bert.aseg.sum >>>>> --in $SUBJECTS_DIR/bert/mri/orig >>>>> >>>>> is the --seg flag necessary in order to calculate only the mean >>>>> intensity >>>>> within the skull, or does it serve another purpose? >>>> The seg defines the segmentations (eg, 17 is hippocampus) >>>> >>>>> Thanks in advance, >>>>> Panos >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu 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 Freesurfer@nmr.mgh.harvard.edu 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.
