subject:"\[Freesurfer\] Mean intensity with mri_segstats \: different results with .annot or .label"

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

2016-11-14 Thread Douglas N Greve

You can use fscalc to multiply the pet and area maps,eg

fscalc pet.lh.nii.gz mul lh.white.avg.area.mgh -o weighted.nii.gz


On 11/14/2016 11:53 AM, Matthieu Vanhoutte wrote:
> Ok I will try both.
>
> Best,
> Matthieu
>
> 2016-11-14 17:50 GMT+01:00 Douglas N Greve  >:
>
> If you did not smooth them explicitly, then there will be only a
> little
> vertex-like smoothing. As to which weighting is better, I'm not
> sure. If
> the ROI is big, it probably won't make much difference. Can you
> try both
> and see?
>
>
> On 11/14/2016 11:39 AM, Matthieu Vanhoutte wrote:
> > Dear Douglas,
> >
> > As I am working on fsaverage with statistical maps, I supposed they
> > are smoothed ?
> >
> > Do I still have to weighting by area ?
> >
> > Best regards,
> > Matthieu
> >
> > 2016-11-14 17:08 GMT+01:00 Douglas N Greve
> 
> >  >>:
> >
> > Good question. I'm not sure as there could be reasons to do
> either. I
> > guess if you are not smoothing your data, then weighting by
> area would
> > be the most appropriate
> >
> > doug
> >
> >
> >
> > On 11/11/2016 05:41 PM, Matthieu Vanhoutte wrote:
> > >
> > > Is it better to compute mean to weight by number of
> vertices or
> > > surface area ?
> > >
> > > Best,
> > > Matthieu
> > >
> > >
> > > Le 11 nov. 2016 11:33 PM, "Douglas N Greve"
> >  
> >
> > >  
> >   > >
> > > 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"
> > >  
> >  >
> >  
> >>
> > > >  
> >
> > >  
> >   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"
> > > >  
> >  >
> > >

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

2016-11-14 Thread Douglas N Greve

If you did not smooth them explicitly, then there will be only a little 
vertex-like smoothing. As to which weighting is better, I'm not sure. If 
the ROI is big, it probably won't make much difference. Can you try both 
and see?


On 11/14/2016 11:39 AM, Matthieu Vanhoutte wrote:
> Dear Douglas,
>
> As I am working on fsaverage with statistical maps, I supposed they 
> are smoothed ?
>
> Do I still have to weighting by area ?
>
> Best regards,
> Matthieu
>
> 2016-11-14 17:08 GMT+01:00 Douglas N Greve  >:
>
> Good question. I'm not sure as there could be reasons to do either. I
> guess if you are not smoothing your data, then weighting by area would
> be the most appropriate
>
> doug
>
>
>
> On 11/11/2016 05:41 PM, Matthieu Vanhoutte wrote:
> >
> > Is it better to compute mean to weight by number of vertices or
> > surface area ?
> >
> > Best,
> > Matthieu
> >
> >
> > Le 11 nov. 2016 11:33 PM, "Douglas N Greve"
> 
> >  >> a écrit :
> >
> > 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"
> >  
> >
> > >  
> >   > >
> > > 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"
> > >  
> >  >
> >  
> >>
> > > >  
> >  >
> > >  
> >   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

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

2016-11-14 Thread Douglas N Greve

Good question. I'm not sure as there could be reasons to do either. I 
guess if you are not smoothing your data, then weighting by area would 
be the most appropriate

doug



On 11/11/2016 05:41 PM, Matthieu Vanhoutte wrote:
>
> Is it better to compute mean to weight by number of vertices or 
> surface area ?
>
> Best,
> Matthieu
>
>
> Le 11 nov. 2016 11:33 PM, "Douglas N Greve"  > a écrit :
>
> 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"
> 
> >  >> 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"
> >  
> >
> > >  
> >   > >
> > > 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 /

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

2016-11-11 Thread Matthieu Vanhoutte

Is it better to compute mean to weight by number of vertices or surface
area ?

Best,
Matthieu

Le 11 nov. 2016 11:33 PM, "Douglas N Greve"  a
écrit :

> 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"  > > 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"
> > 
> > >  > >> 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 1151011510.0  Seg0001  7.6819  1.4396
> > > > 4.486210.9042 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
> > > >>  > 
> > >  > >
> > >  > 
> > >  >

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

2016-11-11 Thread Douglas N Greve

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"  > 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"
> 
> >  >> 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 1151011510.0  Seg0001  7.6819  1.4396
> > > 4.486210.9042 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
> > >>  
> >  >
> >  
> >   > >> écrit :
> > >>
> > >> Thank you Douglas !
> > >>
> > >>
> > >> Le 10 nov. 2016 7:21 PM, "Douglas N Greve"
> >  
> >
> > >>  
> >

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

2016-11-11 Thread Matthieu Vanhoutte

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"  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"  > 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 1151011510.0  Seg0001 7.6819  1.4396
> > 4.486210.9042 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
> >>  
>  >> a
> >> écrit :
> >>
> >> Thank you Douglas !
> >>
> >>
> >> Le 10 nov. 2016 7:21 PM, "Douglas N Greve"
> 
> >>  >> 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
> >> >  
> >>  >
> >>  
> >>   >> >
> >> > Dear experts,
> >> >
> >> > I am in trouble with

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

2016-11-11 Thread Douglas N Greve

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"  > 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 1151011510.0  Seg0001 7.6819  1.4396
> > 4.486210.9042 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
> >>  
>  >> a
> >> écrit :
> >>
> >> Thank you Douglas !
> >>
> >>
> >> Le 10 nov. 2016 7:21 PM, "Douglas N Greve"
> 
> >>  >> 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
> >> >  
> >>  >
> >>  
> >>   >> >
> >> > 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) :
> >> >
> >> >

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

2016-11-11 Thread Matthieu Vanhoutte

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"  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 1151011510.0  Seg0001 7.6819 1.4396
> > 4.486210.9042 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
> >> > a
> >> écrit :
> >>
> >> Thank you Douglas !
> >>
> >>
> >> Le 10 nov. 2016 7:21 PM, "Douglas N Greve"  >> > 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
> >> >  >> 
> >>  >> >>:
> >> >
> >> > 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 2780514182.6  cluster-001 8.8194 1.4351
> >> > 6.210514.2947 8.0842
> >> > 2   2  2321 1047.3  cluster-002  10.3661 1.0848
> >> > 8.837512.9317 4.0942
> >> > 3   3   552  313.1  cluster3 10.3365 0.4711
> >> > 9.371911.8694 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 /
> >> > /
> >> > /
> >> >

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

2016-11-11 Thread Douglas N Greve

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 1151011510.0  Seg0001 7.6819 1.4396 
> 4.486210.9042 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 
>> > a 
>> écrit :
>>
>> Thank you Douglas !
>>
>>
>> Le 10 nov. 2016 7:21 PM, "Douglas N Greve" > > 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
>> > > 
>> > >>:
>> >
>> > 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 2780514182.6  cluster-001 8.8194 1.4351
>> > 6.210514.2947 8.0842
>> > 2   2  2321 1047.3  cluster-002  10.3661 1.0848
>> > 8.837512.9317 4.0942
>> > 3   3   552  313.1  cluster3 10.3365 0.4711
>> > 9.371911.8694 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 8.96371.4701 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

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

2016-11-11 Thread Matthieu Vanhoutte

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 1151011510.0  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  a 
> écrit :
> 
> Thank you Douglas !
> 
> 
> Le 10 nov. 2016 7:21 PM, "Douglas N Greve"  > 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
> >  
> > >>:
> >
> > 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 2780514182.6  cluster-001  8.8194 1.4351
> > 6.210514.2947 8.0842
> > 2   2  2321 1047.3  cluster-002 10.3661 1.0848
> > 8.837512.9317 4.0942
> > 3   3   552  313.1  cluster3  10.3365 0.4711
> > 9.371911.8694 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 
> > 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:

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

2016-11-10 Thread Matthieu Vanhoutte

Thank you Douglas !

Le 10 nov. 2016 7:21 PM, "Douglas N Greve"  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
> > >:
> >
> > 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 2780514182.6  cluster-001  8.8194 1.4351
> > 6.210514.2947 8.0842
> > 2   2  2321 1047.3  cluster-002 10.3661 1.0848
> > 8.837512.9317 4.0942
> > 3   3   552  313.1  cluster3  10.3365 0.4711
> > 9.371911.8694 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
> > 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
>
>
> 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 . 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
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 . 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.

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

2016-11-10 Thread Douglas N Greve

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 
> >:
>
> 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 2780514182.6  cluster-001  8.8194 1.4351
> 6.210514.2947 8.0842
> 2   2  2321 1047.3  cluster-002 10.3661 1.0848
> 8.837512.9317 4.0942
> 3   3   552  313.1  cluster3  10.3365 0.4711
> 9.371911.8694 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
> 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


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 . 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.

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

2016-11-10 Thread Matthieu Vanhoutte

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 :

> 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 2780514182.6  cluster-0018.8194
>   1.4351 6.210514.2947 8.0842
>   2   2  2321 1047.3  cluster-002   10.3661
>   1.0848 8.837512.9317 4.0942
>   3   3   552  313.1  cluster3  10.3365
>   0.4711 9.371911.8694 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 3067815542.9  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
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 . 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.

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

2016-08-16 Thread Matthieu Vanhoutte

Hello FS's experts,

Would anyone have an advice for my problem ?

Best regards,
Matthieu

2016-08-12 12:07 GMT+02:00 Matthieu Vanhoutte :

> 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 2780514182.6  cluster-0018.8194
>   1.4351 6.210514.2947 8.0842
>   2   2  2321 1047.3  cluster-002   10.3661
>   1.0848 8.837512.9317 4.0942
>   3   3   552  313.1  cluster3  10.3365
>   0.4711 9.371911.8694 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 3067815542.9  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
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 . 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] Mean intensity with mri_segstats : different results with .annot or .label

2016-08-12 Thread Matthieu Vanhoutte

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 2780514182.6  cluster-0018.8194
1.4351 6.210514.2947 8.0842
  2   2  2321 1047.3  cluster-002   10.3661
1.0848 8.837512.9317 4.0942
  3   3   552  313.1  cluster3  10.3365
0.4711 9.371911.8694 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 3067815542.9  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
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 . 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.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

15 matches

Site Navigation

Mail list logo

Footer information