Vertices do not have equal areas and are not equally spaced
On 11/11/2016 05:11 PM, Matthieu Vanhoutte wrote: > > Thank you Douglas for giving me a way to compute area from segmented > surface data. > > Are vertices equally spaced along cortex or do triangles all have same > area ? > > Best, > Matthieu > > > Le 11 nov. 2016 10:55 PM, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> a écrit : > > If you want to do it on fsaverage, then > > mris_segstats --i $SUBJECTS/fsaverage/surf/lh.white.avg.area.mgh --seg > lh.sign_clust.bin.mgh > --excludeid 0 --sum lh.bin.area.sum --accumulate > > > > > On 11/11/2016 04:48 PM, Matthieu Vanhoutte wrote: > > > > Dear Douglas, > > > > Yes I would like to in order to compute mean of some means. > Maybe not > > if it is equivalent to number of vertices (are vertices distributed > > equaly distant on the cortical surface ?) > > > > In case I need surface area, do I have to convert overlay to > > annotation file to be used with mri_segstats ? > > > > Best regards, > > Matthieu > > > > > > Le 11 nov. 2016 9:21 PM, "Douglas N Greve" > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> a écrit : > > > > NVox is the number of vertices. The Volume_mm3 is not > meaningful. > > Do you > > want area? > > > > > > On 11/11/2016 04:53 AM, Matthieu Vanhoutte wrote: > > > Dear Douglas, > > > > > > I come back to you concerning stats made from binary .mgh > > surface data > > > file: > > > > > > mri_segstats --i lh.fsaverage.sm10.mgh --seg > lh.sign_clust.bin.mgh > > > --excludeid 0 --sum lh.bin.sum --avgwf lh.wav.bin.txt > > > > > > In the output file « lh.bin.sum » all is considered as volume > > > input/output as you could see below: > > > > > > /# InVolFileTimeStamp 2016/04/28 09:46:19 / > > > /# InVolFrame 0 / > > > /# ExcludeSegId 0 / > > > /# Only reporting non-empty segmentations/ > > > /# VoxelVolume_mm3 1 / > > > /# TableCol 1 ColHeader Index / > > > /# TableCol 1 FieldName Index / > > > /# TableCol 1 Units NA / > > > /# TableCol 2 ColHeader SegId / > > > /# TableCol 2 FieldName Segmentation Id/ > > > /# TableCol 2 Units NA/ > > > /# TableCol 3 ColHeader NVoxels / > > > /# TableCol 3 FieldName Number of Voxels/ > > > /# TableCol 3 Units unitless/ > > > /# TableCol 4 ColHeader Volume_mm3/ > > > /# TableCol 4 FieldName Volume/ > > > /# TableCol 4 Units mm^3/ > > > /# TableCol 5 ColHeader Mean / > > > /# TableCol 5 FieldName Intensity Mean/ > > > /# TableCol 5 Units unknown/ > > > /# TableCol 6 ColHeader StdDev/ > > > /# TableCol 6 FieldName Itensity StdDev/ > > > /# TableCol 6 Units unknown/ > > > /# TableCol 7 ColHeader Min/ > > > /# TableCol 7 FieldName Intensity Min/ > > > /# TableCol 7 Units unknown/ > > > /# TableCol 8 ColHeader Max/ > > > /# TableCol 8 FieldName Intensity Max/ > > > /# TableCol 8 Units unknown/ > > > /# TableCol 9 ColHeader Range/ > > > /# TableCol 9 FieldName Intensity Range/ > > > /# TableCol 9 Units unknown/ > > > /# NRows 1 / > > > /# NTableCols 9 / > > > /# ColHeaders Index SegId NVoxels Volume_mm3 StructName > Mean StdDev > > > Min Max Range / > > > / 1 1 11510 11510.0 Seg0001 7.6819 1.4396 > > > 4.4862 10.9042 6.4180 / > > > > > > As my inputs are all surface data could I consider that > NVoxels is > > > equal to NVertices and Volume_mm3 is equal to > SurfaceArea_mm2 ? > > > > > > Best regards, > > > Matthieu > > > > > >> Le 10 nov. 2016 à 23:18, Matthieu Vanhoutte > > >> <matthieuvanhou...@gmail.com > <mailto:matthieuvanhou...@gmail.com> > > <mailto:matthieuvanhou...@gmail.com > <mailto:matthieuvanhou...@gmail.com>> > > <mailto:matthieuvanhou...@gmail.com > <mailto:matthieuvanhou...@gmail.com> > > <mailto:matthieuvanhou...@gmail.com > <mailto:matthieuvanhou...@gmail.com>>>> a > > >> écrit : > > >> > > >> Thank you Douglas ! > > >> > > >> > > >> Le 10 nov. 2016 7:21 PM, "Douglas N Greve" > > <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> > > >> <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>>> a écrit : > > >> > > >> You need to weight by the number of vertices > > >> > > >> n = [27805 2321 552]; > > >> m = [8.8194 10.3661 10.3365]; > > >> sum(n.*m)/sum(n) > > >> > > >> ans = > > >> > > >> 8.9637 > > >> > > >> > > >> On 11/10/2016 06:44 AM, Matthieu Vanhoutte wrote: > > >> > Dear Freesurfer's experts, > > >> > > > >> > Could anyone please explain me the difference I got > with > > >> command line > > >> > in below mail ? > > >> > > > >> > Best regards, > > >> > Matthieu > > >> > > > >> > 2016-08-12 12:07 GMT+02:00 Matthieu Vanhoutte > > >> > <matthieuvanhou...@gmail.com > <mailto:matthieuvanhou...@gmail.com> > > <mailto:matthieuvanhou...@gmail.com > <mailto:matthieuvanhou...@gmail.com>> > > >> <mailto:matthieuvanhou...@gmail.com > <mailto:matthieuvanhou...@gmail.com> > > <mailto:matthieuvanhou...@gmail.com > <mailto:matthieuvanhou...@gmail.com>>> > > >> <mailto:matthieuvanhou...@gmail.com > <mailto:matthieuvanhou...@gmail.com> > > <mailto:matthieuvanhou...@gmail.com > <mailto:matthieuvanhou...@gmail.com>> > > >> <mailto:matthieuvanhou...@gmail.com > <mailto:matthieuvanhou...@gmail.com> > > <mailto:matthieuvanhou...@gmail.com > <mailto:matthieuvanhou...@gmail.com>>>>>: > > >> > > > >> > Dear experts, > > >> > > > >> > I am in trouble with two ways of computing mean > > intensity with > > >> > mri_segstats. > > >> > > > >> > First I have used on .annot files with three > > different labels > > >> > inside (SegId 1 to 3) : > > >> > > > >> > /mri_segstats --annot fsaverage lh > > cache.th23.pos.sig.ocn.annot > > >> > --i lh.PET.fsaverage.sm10.mgh --sum lh.pet.sum/ > > >> > / > > >> > / > > >> > which give me those results: > > >> > # ColHeaders Index SegId NVertices Area_mm2 > > StructName Mean > > >> > StdDev Min Max Range > > >> > 1 1 27805 14182.6 cluster-001 8.8194 > 1.4351 > > >> > 6.2105 14.2947 8.0842 > > >> > 2 2 2321 1047.3 cluster-002 10.3661 > > 1.0848 > > >> > 8.8375 12.9317 4.0942 > > >> > 3 3 552 313.1 cluster3 10.3365 > 0.4711 > > >> > 9.3719 11.8694 2.4975 > > >> > > > >> > Second I have created on .label files > containing the > > three > > >> > segmented labels (SegId 1 to 3) and used this > label with > > >> mri_segstats: > > >> > > > >> > /mri_segstats --slabel fsaverage lh > > >> > lh.th23.cluster.thresh1.3.label --i > > lh.PET.fsaverage.sm10.mgh > > >> > --excludeid 0 --sum lh.pet.label.sum / > > >> > / > > >> > / > > >> > which give me those results:/ > > >> > / > > >> > /# ColHeaders Index SegId NVertices Area_mm2 > > StructName Mean > > >> > StdDev Min Max Range / > > >> > / 1 1 30678 15542.9 Seg0001 8.9637 > 1.4701 > > 6.2105 > > >> > 14.2947 8.0842 / > > >> > / > > >> > / > > >> > I verified if I obtained the same results with the > > two ways > > >> > (.annot or .label) and everything is fine comparing > > NVertices, > > >> > Area_mm2 but Mean in first way gives me > > >> (8.8194+10.3661+10.3365)/3 > > >> > = 9.84066 and with .label file Mean = 8.9637. > > >> > > > >> > Did I have miss anything and how is computed mean > > intensity ? > > >> > > > >> > Many thanks in advance. > > >> > > > >> > Best regards, > > >> > Matthieu > > >> > > > >> > > > >> > > > >> > > > >> > _______________________________________________ > > >> > Freesurfer mailing list > > >> > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > >> <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > >> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > > >> > > >> -- > > >> Douglas N. Greve, Ph.D. > > >> MGH-NMR Center > > >> gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>> > > >> Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > > >> Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 > <tel:617-726-7422> > > <tel:617-726-7422 <tel:617-726-7422>>> > > >> > > >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > > >> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>> > > >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > > <https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2>> > > >> <https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > > <https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2>>> > > >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > > >> > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>> > > >> Outgoing: > > >> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > > >> > > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>> > > >> > > >> _______________________________________________ > > >> Freesurfer mailing list > > >> Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > >> <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > >> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <http://www.partners.org/complianceline> > > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline>> > > >> <http://www.partners.org/complianceline > <http://www.partners.org/complianceline> > > <http://www.partners.org/complianceline > <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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > > <https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2>> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > _______________________________________________ > 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 gr...@nmr.mgh.harvard.edu 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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
