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
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 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
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:
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
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>:
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you Douglas !
Le 10 nov. 2016 7:21 PM, "Douglas N Greve" 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 =
8.9637On 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>:
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 withmri_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 greve@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/
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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.
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 =
8.9637On 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/
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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.
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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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 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> 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 lhcache.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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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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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 >> > >> > >> > >> > >> > _______________________________________________ >> > 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 >> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 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>
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Douglas N Greve -
Matthieu Vanhoutte