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, pfot...@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, 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
>>>>>
>>>>>
>>>>>
>>>> _______________________________________________
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>>>>
>>> --
>>> 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
>>>
>>>
>>>
>> _______________________________________________
>> 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
>
>
>
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