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, pfotiad@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, pfotiad@nmr.mgh.harvard.edu wrote:
Hi Doug,
Thanks for the quick reply! In addition:
- 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.
- 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, pfotiad@nmr.mgh.harvard.edu wrote:
Hi FS community,
I had some questions regarding the mri_segstats command:
- In the excludeid flag, are the ids the ones shown in the
FreeSurferColorLUT.txt?
Yes
- 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
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