________________________________________ 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
Universitätsklinikum Heidelberg
Zentrum für Psychosoziale Medizin
Klinik für Allgemeine Psychiatrie
Sektion für Gerontopsychiatrie
Voßstr. 4
69115 Heidelberg
Tel.: +49 (0) 6221 - 56 7578
Email: iven.fellhauer@med.uni-heidelberg.de
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. _______________________________________________ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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 [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
Universitätsklinikum Heidelberg
Zentrum für Psychosoziale Medizin
Klinik für Allgemeine Psychiatrie
Sektion für Gerontopsychiatrie
Voßstr. 4
69115 Heidelberg
Tel.: +49 (0) 6221 - 56 7578
Email: iven.fellhauer@med.uni-heidelberg.de
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. _______________________________________________ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Fellhauer, Iven