Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

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 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

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-- 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

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