probably easiest to do in matlab:
[v,M,mr] = load_mgh('aseg.mgz');
ind = find(v ~= 17 & v ~= 53 & v ~= 18 & v ~= 54) ;
v(ind) = zeros(size(ind));
save_mgh(v, 'aseg.mtl.mgz', M,mr);
cheers
Bruce
On Thu, 24 May 2012, Martina Butt wrote:
> Thanks for your help, Bruce!
>
> Unfortunately, this also leads to a mgz.file where hippocampus and amygdala
> are "merged" together so that I can't see anymore what is hippocampus and
> what is amygdala (both have same value). I tried some other things but
> nothing appears to work. Any other suggestions?
>
> Many thanks, Martina
>
> Quoting Bruce Fischl <fis...@nmr.mgh.harvard.edu> on Thu, 24 May 2012
> 08:53:14 -0400 (EDT):
>
>> Hi Martina
>> you can use mri_binarize --match 17 --match 18... to do this.
>>
>> cheers
>> Bruce
>>
>>
>>
>> On Thu, 24 May 2012, Martina Papmeyer wrote:
>>
>>> Hello everyone,
>>>
>>> I guess that this might be a simple question but I couldn't find an
>>> answer to my problem yet.
>>>
>>> I would like to extract and visualize four labels from my aseg.mgz
>>> file for illustration purposes. I tried the following:
>>>
>>> mri_extract_label aseg.mgz 17 18 53 54 filename.mgz
>>>
>>> (the values correspond to left/right amygdala and left/right
>>> hippocampus as specified in FreeSurferColorLUT.txt file)
>>>
>>> This command unfortunately combines all the four selected labels
>>> together so that I can't differentiate amygdala and hippocampus
>>> anymore when I load the filename.mgz file together with my
>>> FreeSurferColorLUT.txt file in tkmedit.
>>>
>>> Is there any other FS tool I can use?
>>>
>>> Any form of help would be highly appreciated!
>>>
>>> Many thanks and all best wishes, Martina
>>>
>>>
>>
>>
>> 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.
>
>
>
>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
