[Freesurfer] WG: Save segmentation results as nifi files

________________________________________ Von: Fellhauer, Iven Gesendet: Donnerstag, 15. März 2012 10:29 Bis: Douglas N Greve Betreff: AW: [Freesurfer] WG: Save segmentation results as nifi files

Dear all,

in which space are the output files stored? If they are not stored in MNI space, which steps are necessary to convert these images into MNI space.

Best regards,

Iven Fellhauer

________________________________________ Von: Douglas N Greve [greve@nmr.mgh.harvard.edu] Gesendet: Dienstag, 31. Januar 2012 18:33 Bis: Fellhauer, Iven Cc: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] WG: Save segmentation results as nifi files

There's not a separate GM, WM, and CSF. You can create these from the segmentations with mri_binarize. In general, it is run something like this:

mri_binarize --i aparc+aseg.mgz --match id1 id2 --o output.nii where id1 and id2 are structure codes from $FREESURFER_HOME/FreeSurferColorLUT.txt

For all WM use: 2, 41, 77, 7, 46, 251-255 For all ventricular CSF and choroid plexus use: 4, 5, 14, 45, 44, 72, 31, 63, 15 For GM, use all the above plus 0, then add the --inv option to invert the mask (basically creating a mask of everything that is not GM and inverting it).

doug

Fellhauer, Iven wrote:

Hi Bruce

And thank you for your hint, but where are the files for GM, WM and CFS stored in the Freesurfer output directory structur?

Best regards,

Iven

-----Ursprüngliche Nachricht----- Von: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Gesendet: Montag, 30. Januar 2012 15:20 An: Fellhauer, Iven Cc: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Save segmentation results as nifi files

Hi Ivan

you can convert any volume to any supported output type using mri_convert. It will figure out the format from the extension, so:

mri_convert aseg.mgz aseg.nii.gz

or

mri_convert aseg.mgz aseg.nii

should do the trick

cheers Bruce

On Mon, 30 Jan 2012, Fellhauer, Iven wrote:

...

Dear all,

I run recon-all with the ?autorecon1 and ?autorecon2 options. Now I want to store the segmentation results in a spm like way. One nifti file for each matter. Can I do this with freesurfer? And how can I do this with freesurfer?

Best regards,

Iven Fellhauer

---

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