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 <matthieuvanhoutte@gmail.com mailto:matthieuvanhoutte@gmail.com> a écrit :
Thank you Douglas !
Le 10 nov. 2016 7:21 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edu mailto:greve@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 > <matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@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> > 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 greve@nmr.mgh.harvard.edu <mailto:greve@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> 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> . 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.
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