Hi! I have a volume in MNC format that contains labels, and I was wondering whether there is a way to quickly convert them into Freesurfer labels? Within the MNC file, voxels belonging to one label all have the same intensity value, which is, however, not in RGB space but just a single number, ranging from 1 to the number of labels. Thanks, Caspar
Hi Caspar,
One thing you can do, if you have the label correspondences between your lables and the FS ones, is to use mri_binarize with the --replace option in your volumes.
--replace V1 V2 : replace voxels=V1 with V2
For label descriptions you can loook up $FREESURFER_HOME/FreeSurferColorLUT.txt.
--Lilla
On Mon, 6 Jan 2014, Caspar M. Schwiedrzik wrote:
Hi! I have a volume in MNC format that contains labels, and I was wondering whether there is a way to quickly convert them into Freesurfer labels? Within the MNC file, voxels belonging to one label all have the same intensity value, which is, however, not in RGB space but just a single number, ranging from 1 to the number of labels. Thanks, Caspar
Hi Lilla, unfortunately, there is no correspondence between the Freesurfer labels and the labels in the MNC volume at this point. I would simply like to convert each label in the MNC file to a new Freesurfer label file. Caspar
2014/1/6 Lilla Zollei lzollei@nmr.mgh.harvard.edu
Hi Caspar,
One thing you can do, if you have the label correspondences between your lables and the FS ones, is to use mri_binarize with the --replace option in your volumes.
--replace V1 V2 : replace voxels=V1 with V2
For label descriptions you can loook up $FREESURFER_HOME/ FreeSurferColorLUT.txt.
--Lilla
On Mon, 6 Jan 2014, Caspar M. Schwiedrzik wrote:
Hi!
I have a volume in MNC format that contains labels, and I was wondering whether there is a way to quickly convert them into Freesurfer labels? Within the MNC file, voxels belonging to one label all have the same intensity value, which is, however, not in RGB space but just a single number, ranging from 1 to the number of labels. Thanks, Caspar
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Than you can use mri_binarize with the --match flag.
--match matchval
--Lilla
On Mon, 6 Jan 2014, Caspar M. Schwiedrzik wrote:
Hi Lilla, unfortunately, there is no correspondence between the Freesurfer labels and the labels in the MNC volume at this point. I would simply like to convert each label in the MNC file to a new Freesurfer label file. Caspar
2014/1/6 Lilla Zollei lzollei@nmr.mgh.harvard.edu
Hi Caspar, One thing you can do, if you have the label correspondences between your lables and the FS ones, is to use mri_binarize with the --replace option in your volumes. --replace V1 V2 : replace voxels=V1 with V2 For label descriptions you can loook up $FREESURFER_HOME/FreeSurferColorLUT.txt. --Lilla On Mon, 6 Jan 2014, Caspar M. Schwiedrzik wrote: Hi! I have a volume in MNC format that contains labels, and I was wondering whether there is a way to quickly convert them into Freesurfer labels? Within the MNC file, voxels belonging to one label all have the same intensity value, which is, however, not in RGB space but just a single number, ranging from 1 to the number of labels. Thanks, CasparThe 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.
Hi Caspar
can you describe in more detail what you are trying to do. Do you mean to sample each unique label into a surface label format? Do you have surfaces for this subject?
cheers Bruce On Mon, 6 Jan 2014, Caspar M. Schwiedrzik wrote:
Hi Lilla, unfortunately, there is no correspondence between the Freesurfer labels and the labels in the MNC volume at this point. I would simply like to convert each label in the MNC file to a new Freesurfer label file. Caspar
2014/1/6 Lilla Zollei lzollei@nmr.mgh.harvard.edu
Hi Caspar, One thing you can do, if you have the label correspondences between your lables and the FS ones, is to use mri_binarize with the --replace option in your volumes. --replace V1 V2 : replace voxels=V1 with V2 For label descriptions you can loook up $FREESURFER_HOME/FreeSurferColorLUT.txt. --Lilla On Mon, 6 Jan 2014, Caspar M. Schwiedrzik wrote: Hi! I have a volume in MNC format that contains labels, and I was wondering whether there is a way to quickly convert them into Freesurfer labels? Within the MNC file, voxels belonging to one label all have the same intensity value, which is, however, not in RGB space but just a single number, ranging from 1 to the number of labels. Thanks, CasparThe 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.
Hi Bruce and Lilla, I have a MNC volume that contains area labels, ie voxels belonging to one label all have the same intensity value. I am trying to get this converted into Freesurfer label files for further analysis in volume space. Following Lilla's advice, I am first using mri_binarize with --match. I figured that I can then use mri_cor2label with --id 1 to get a label file from the binary mask, correct? There seem to be some individual voxels outside the labeled area that have the same values as the label; they are scattered across the volume. Is there a way to cluster size threshold the binarized mask? Thanks, Caspar
2014/1/6 Bruce Fischl fischl@nmr.mgh.harvard.edu
Hi Caspar
can you describe in more detail what you are trying to do. Do you mean to sample each unique label into a surface label format? Do you have surfaces for this subject?
cheers Bruce
On Mon, 6 Jan 2014, Caspar M. Schwiedrzik wrote:
Hi Lilla,
unfortunately, there is no correspondence between the Freesurfer labels and the labels in the MNC volume at this point. I would simply like to convert each label in the MNC file to a new Freesurfer label file. Caspar
2014/1/6 Lilla Zollei lzollei@nmr.mgh.harvard.edu
Hi Caspar, One thing you can do, if you have the label correspondences between your lables and the FS ones, is to use mri_binarize with the --replace option in your volumes. --replace V1 V2 : replace voxels=V1 with V2 For label descriptions you can loook up $FREESURFER_HOME/FreeSurferColorLUT.txt. --Lilla On Mon, 6 Jan 2014, Caspar M. Schwiedrzik wrote: Hi! I have a volume in MNC format that contains labels, and I was wondering whether there is a way to quickly convert them into Freesurfer labels? Within the MNC file, voxels belonging to one label all have the same intensity value, which is, however, not in RGB space but just a single number, ranging from 1 to the number of labels. Thanks, CasparThe 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@nmr.mgh.harvard.edu