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 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.
