I mean anatomical.nii.gz with the same spatial features of the masks.

Thanks, 


Stefano

----Messaggio originale----
Da: stdp82@virgilio.it
Data: 4-set-2013 23.02
A: <greve@nmr.mgh.harvard.edu>, <freesurfer@nmr.mgh.harvard.edu>
Ogg: [Freesurfer] R: Re: Mask from cortical parcellation

Thank you very much.

A last help, please. How is the anatomical file that I can use to overlay the masks. I'm noting that masks are characterized by:
data_type      INT32
dim1           256
dim2           256
dim3           256
dim4           1
datatype       8
pixdim1        1.0000000000
pixdim2        1.0000000000
pixdim3        1.0000000000
pixdim4        0.0109999999
cal_max        0.0000
cal_min        0.0000
file_type      NIFTI-1+

Regards,


Stefano

----Messaggio originale----
Da: greve@nmr.mgh.harvard.edu
Data: 4-set-2013 17.10
A: <freesurfer@nmr.mgh.harvard.edu>
Ogg: Re: [Freesurfer] Mask from cortical parcellation



you can use mri_binarize on aparc+aseg, eg, something like

mri_binarize --i aparc+aseg.mgz --match 1003 1012 1014 1032 --o
frontal.nii.gz

those numbers come from  $FREESURFER_HOME/FreeSurferColorLUT.txt
That table has a lot of ROIs in it, and not all will be in the
aparc+aseg. You'll be interested in the ones between 1000-1035 and 2000-2035

doug




On 09/04/2013 08:46 AM, stdp82@virgilio.it wrote:
> Hi list,
>
> I need to create a mask of frontal, parietal, temporal and occipital
> lobes in a subject by using cortical parcellation output.
>
> Is it possible? Eventually, how can I transform these masks file to
> mii.gz (to import them in FSL analysis).
>
> Thank you very much.
>
> Regards,
>
>
> Stefano
>
>
>
>
>
> _______________________________________________
> 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
greve@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


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.