Re: [Freesurfer] Question about hippocampal-subfield probability map
Hi Joshua, The correct way to obtain binarized maps would be to visit each voxel in turn, compute the probability that it belongs to each of the subfieds, and pick the subfield with the highest such probability. Having said that, it should not be the case that there are two or more subfields with value 150 in any voxel. I'm representing probabilities with numbers between 0 and 255 to save disk space, and while this may introduce some rounding off errors, the sum over all subfields should still sum to something around 255 (unless there is a big bug in my code)... Koen On Tue, Feb 14, 2012 at 6:59 PM, Joshua Lee jki...@ucdavis.edu wrote: Dear experts, The hippocampal-subfield are expressed as probability maps. For each subfield, each voxel is assigned a probability of inclusion on a scale of [0-255]=[0-1]. However, If I were to select only voxels from each subfield's probability map corresponding to a 50% chance (i.e. mri_binarize -min 150), then I would expect that no subfield would overlap with another (i.e. a voxel shouldn't have greater than 50% probability of belonging CA1, AND a greater than 50% probability of belonging to CA4-DG. However it appears that this is not the case, and overlap does occur. Thus, unless I messed up, subfields are not mutually exclusive. Have I got this right? And if so, how do I obtain binary maps of subfields with no overlap? Thanks Josh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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
[Freesurfer] Question about hippocampal-subfield probability map
Dear experts, The hippocampal-subfield are expressed as probability maps. For each subfield, each voxel is assigned a probability of inclusion on a scale of [0-255]=[0-1]. However, If I were to select only voxels from each subfield's probability map corresponding to a 50% chance (i.e. mri_binarize -min 150), then I would expect that no subfield would overlap with another (i.e. a voxel shouldn't have greater than 50% probability of belonging CA1, AND a greater than 50% probability of belonging to CA4-DG. However it appears that this is not the case, and overlap does occur. Thus, unless I messed up, subfields are not mutually exclusive. Have I got this right? And if so, how do I obtain binary maps of subfields with no overlap? Thanks Josh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Question about hippocampal-subfield probability map
Ha nevermind. While true, I can just mask the masks with each other and drop the over lapped regions. - Josh On Tue, Feb 14, 2012 at 3:59 PM, Joshua Lee jki...@ucdavis.edu wrote: Dear experts, The hippocampal-subfield are expressed as probability maps. For each subfield, each voxel is assigned a probability of inclusion on a scale of [0-255]=[0-1]. However, If I were to select only voxels from each subfield's probability map corresponding to a 50% chance (i.e. mri_binarize -min 150), then I would expect that no subfield would overlap with another (i.e. a voxel shouldn't have greater than 50% probability of belonging CA1, AND a greater than 50% probability of belonging to CA4-DG. However it appears that this is not the case, and overlap does occur. Thus, unless I messed up, subfields are not mutually exclusive. Have I got this right? And if so, how do I obtain binary maps of subfields with no overlap? Thanks Josh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Question about hippocampal-subfield probability map
That is, I can use fslmaths from fsl suite to subtract my binarized subfield rois. - Josh On Tue, Feb 14, 2012 at 4:58 PM, Joshua Lee jki...@ucdavis.edu wrote: Ha nevermind. While true, I can just mask the masks with each other and drop the over lapped regions. - Josh On Tue, Feb 14, 2012 at 3:59 PM, Joshua Lee jki...@ucdavis.edu wrote: Dear experts, The hippocampal-subfield are expressed as probability maps. For each subfield, each voxel is assigned a probability of inclusion on a scale of [0-255]=[0-1]. However, If I were to select only voxels from each subfield's probability map corresponding to a 50% chance (i.e. mri_binarize -min 150), then I would expect that no subfield would overlap with another (i.e. a voxel shouldn't have greater than 50% probability of belonging CA1, AND a greater than 50% probability of belonging to CA4-DG. However it appears that this is not the case, and overlap does occur. Thus, unless I messed up, subfields are not mutually exclusive. Have I got this right? And if so, how do I obtain binary maps of subfields with no overlap? Thanks Josh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
