Thank you Douglas for giving me a way to compute area from segmented surface data.

Le 11 nov. 2016 10:55 PM, "Douglas N Greve" <greve@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" <greve@nmr.mgh.harvard.edu

> <mailto:greve@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
> >> <matthieuvanhoutte@gmail.com
> <mailto:matthieuvanhoutte@gmail.com>

> <mailto: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>

> >> <mailto: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>>
> >> <mailto: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
> >> >
> >> >
> >> >
> >> >
> >> > _______________________________________________
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> >> --
> >> Douglas N. Greve, Ph.D.
> >> MGH-NMR Center
> >> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>

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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
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--
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MGH-NMR Center
greve@nmr.mgh.harvard.edu
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