That is great, Thanks a lot, Doug!
You can just do it in matlab, somethhing like
a = MRIread('aparc+aseg.mgz'); ind = find(a.vol > 999); a.vol(ind) = 0; MRIwrite(a,'nocortex.mgz')
On 04/22/2014 11:38 AM, pfotiad@nmr.mgh.harvard.edu wrote:
Hi Doug,
I'm sorry, what I meant to ask in the previous question is whether there is a way to come up with a segmentation volume for the mri_segstats command that is exactly like aseg.mgz but that does not include the cortex. The reason I'm asking is because by using the aseg.mgz volume in the --seg flag, you're also incorporating the intensity of the cortex when measuring the mean intensity of orig.mgz, but I wanted to see if there was a way to calculate the mean intensity of orig.mgz but without incorporating the intensity of the cortex.
Thanks again, Panos
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: >> >> 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
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