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> 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>> 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>>> 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>>> 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>>>>: > >> > > >> > 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>> > >> > > 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>> > >> > >> > >> 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>> . 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> > > 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 <tel:617-724-2358> > Fax: 617-726-7422 <tel: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. 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