I'd like to perform probtrackx (FSL) from seed (subcortical) to target (cortical) masks.

To this aim, I should trasform all cortical and subcortical masks obtained by FS on MNI space.

Therefore, firstly,  I'd like to overlay the masks that I obtained by mri_binarize on the structural image to check the masks.

Next, I'd like to apply FLIRT to trasform all masks in a common MNI152_1mm space. 

My problem is " which is the T1.nii.gz that can I use to overlay the cortical masks created by mri_binarize?"


Thanks, 


Stefano



----Messaggio originale----
Da: greve@nmr.mgh.harvard.edu
Data: 4-set-2013 23.28
A: <stdp82@virgilio.it>
Cc: <freesurfer@nmr.mgh.harvard.edu>
Ogg: Re: [Freesurfer] R:  R: Re:  Mask from cortical parcellation

I don't understand your question. Can you elaborate?
On 09/04/2013 05:27 PM, stdp82@virgilio.it wrote:
> 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
> >
> >
> >
> >
> >
> > _______________________________________________
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> > 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
>
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--
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
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