they are stored in the native "conformed" anatomical space
On Thu, 15 Mar
2012, Fellhauer, Iven wrote:
________________________________________
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 [gr...@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:fis...@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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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.
