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.
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
Thanks Doug.
Best regards,
Iven
________________________________________ 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@nmr.mgh.harvard.edu
-
Douglas N Greve -
Fellhauer, Iven