Hi Doug -- 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 # hostname rage.uphs.upenn.edu # 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
wrote:
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.**edugreve@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 0 1 81837 81837 <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<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 <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. > > > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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