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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