Thanks very much, Douglas. That is very helpful -- definitely newbie questions ...
Regards, Don Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text > -----Original Message----- > From: [email protected] [mailto:freesurfer- > [email protected]] On Behalf Of Douglas N Greve > Sent: Friday, August 15, 2014 12:22 PM > To: [email protected] > Subject: Re: [Freesurfer] language questions+ > > > On 08/12/2014 01:25 PM, Krieger, Donald N. wrote: > > > > _segmentation vs parcellation_: > > > > Segmentation appears to mean identifying and assigning voxels to a > > label which maps to a gross structure like thalamus, left cortex, etc. > > Parcellation appears to mean the same but for mappings at higher > > resolution, e.g. L V1. Is this correct? > > > Actually, they basically mean the same thing. "segmentation" emerged from > our volume tools and parcellation emerged from our surfaces tools. > The segmentation format is a single index assigned to each voxel that then > indexes a look up table where it gets color and name. The parcellation format > stores an RGB at each vertex, then uses this RGB to index into a LUT to get > the name. > > > > _surface vs volume_: > > > > My questions here arise from differences in the results of extracting > > labels when using mri_cor2label vs mri_annotation2label. > > > > Spot checks of mri_cor2label results show sets of pixels on a 1 mm > > grid which fill the volume associated with the label. > > > > I have been assuming that this is "volume" although volume also refers > > to what is captured in the .mgz files. > > > Right, when a label is derived from a volume, the xyz must be on the grid of > the volume. For surfaces, they must be on the surface mesh, but this is not a > grid. You'll also notice that labels derived from volumes will have -1 as the > first column (the vertex index, which makes no sense for volumes, of course, > so -1) > > > > Spot checks of mri_annotation2label results show sets of pixels which > > appear to delineate boundaries or "surfaces" of the gray matter > > (--surface orig), white matter ( --surface white) or pia (--surface > > pial). > > > > There appears to a similar switch in the help text for mri_cor2label, > > i.e. -surf subject hemi <surf>, but it appears to specify the nature > > of the input rather than that of the output as does the -surface > > switch in mri_annotation2label. This leads to my next question > > regarding the input "volume" but first, is what I've said correct so > > far? An addition concern that I have is that "surface" may be used in > > reference to a projection onto the sphere. > > > This gets back to your first question about segmentation vs parcellation. In > FS, parcellations are always on the surface. However, segementations can be > volume or surface. If you have a segmentation on the surface and want to > create a label, then you use cor2label and spec the --surf. This will fill > the first > column of the label with the vertex number instead of -1 and the xyz will > derive from the surface you give it. > > > > _input volumes_: > > > > Here I have only tried the .mgz files contained in directory > > ${FREESURFER_HOME}/subjects/NNN/mri . > > > > Which of these files are useful as input to mri_cor2label for > > outputting .label files that are likely to accurately fill the > > structures to which the label corresponds? > > > > What I mean here is which ones represent the end-points of a > > processing stream and which ones are intermediates? > > > > I understand that the intermediates are likely useful given that they > > are being saved in the standard processing streams. > > > aseg.mgz for non-cortical structures. For cortical structures, you can use > ?h.aparc.annot (or possibly aparc+aseg.mgz) > > > > If I load them into freeview, specify the standard color map, and > > place the cursor on the cerebellum, I can see which ones give the > > right answer, e.g. aparc.a2009, wmparc, aparc+aseg, aseg.auto, and > > which don't, e.g. filled, wm.seg, wm, rh.ribbin, brain, > > brain.finalsurfs, T1, orig (of course). But "filled", for instance, > > does appear to provide a good segementation of the left and right > > supra-tentorial white matter although the colors (right=127; left=255) > > do not map to those names in the standard color table. > > > filled, brain, brainmask, brain.mask.finalsurfs are intermediate volumes doug > > > > Regards, > > > > Don > > > > Don Krieger, Ph.D. > > > > Department of Neurological Surgery > > > > Universityof Pittsburgh > > > > (412)648-9654 Office > > > > (412)521-4431 Cell/Text > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > [email protected] > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [email protected] > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > [email protected] > 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 . 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