Right, so in this case, the "NVoxels" column is the number of vertices, the "Mean" column is the average surface area of the vertices in the mask. You can force it to compute the total surface area by adding the --accumulate flag. Or you can multiple the mean by the number of vertices.
doug
On 06/11/2013 04:55 PM, Glen Lee wrote:
Hi Doug --# hostname rage.uphs.upenn.edu <http://rage.uphs.upenn.edu>
I copied and pasted the summary file below.
It looks like mask.mgh was treated as volumetric image.
Also I'm not sure how to interpret TableCol.
# Title Segmentation Statistics
#
# generating_program mri_segstats
# cvs_version $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $
# cmdline mri_segstats --seg mask.mgh --id 1 --i /fMRI/2D/freesurfer/fsaverage_sym/surf/lh.area --sum sum.dat
# sysname Linux
# machine x86_64
# user gel
# anatomy_type volume
#
# SegVolFile mask.mgh
# SegVolFileTimeStamp 2013/06/05 14:50:24
# InVolFile /fMRI/2D/freesurfer/fsaverage_sym/surf/lh.area
# InVolFileTimeStamp 2013/05/22 16:49:43
# InVolFrame 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 81837 81837.0 Seg0001 0.3836 0.1111 0.1297 1.1861 1.0563
On Tue, Jun 11, 2013 at 11:44 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:<mailto:greve@nmr.mgh.harvard.edu
Did you look in the summary file? If you have questions about
that, can you send it?
doug
On 06/11/2013 11:34 AM, Glen Lee wrote:
mri_segstats --seg mask.mgh --id 1 --i
/fMRI/2D/freesurfer/fsaverage_sym/surf/lh.area --sum sum.dat
On Tue, Jun 11, 2013 at 10:41 AM, Douglas Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>0 1 81837 81837 <tel:1%2081837%20%2081837>
<mailto:greve@nmr.mgh.harvard.edu>>> wrote:
what is your full command line?
On 6/11/13 10:04 AM, Glen Lee wrote:
thanks Doug.
it worked and I got the following result on which I have
clarifying questions:
--------------
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 1 segmentations
Computing statistics for each segmentation<mailto:greve@nmr.mgh.harvard.edu
<tel:1%20%C2%A0%2081837%20%C2%A081837>
----------------
1) I'm assuming that voxel here refers to vertex since I'm
submitting the surface data.
2) what does 'found 1 segmentations mean'?
3) the dimension is 81837mm^2, correct?
On Tue, Jun 11, 2013 at 12:31 AM, Douglas Greve
<greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>> wrote:
It's --sum for this, not --o
doug
On 6/10/13 4:44 PM, Glen Lee wrote:
Thanks Doug!
I just tried, but I got an error:
mri_segstats --seg mask.mgh --id 1 --i
/fMRI/2D/freesurfer/fsaverage_sym/surf/lh.area
--o sum.dat
ERROR: Option --o unknown
I don't see --o option when I looked up
mri_segstats --help
either. FYI, I'm using v5.1.
Any idea?
On Mon, Jun 10, 2013 at 3:39 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>> wrote:
Hi Glen, you can use
mri_segstats --seg mask.mgh --id 1 --i
$SUBJECTS_DIR/fsaverage_sym/surf/lh.area
--o sum.dat
doug
On 06/10/2013 03:17 PM, Glen Lee wrote:
> Dear freesurfer users
>
> I'm wondering if there is any way of
figuring out the
surface size
> within a mask image (mask.mgh)
> which is generated after running a
group-level GLM
analysis (2nd RFX)
> using mri_glmfit.
>
> As I'm thinking, this may be:
> number of vertex by dimension of one
vertex (1mm).
>
> But I could be wrong and let me know if
anyone knows
the solution.
>
> -Glen
>
> fyi) the group analysis was performed in
freesurfer
sym space.
>
>
>
>
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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
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
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