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 <gr...@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 < >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@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 >>> <gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@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 >>>> <gr...@nmr.mgh.harvard.edu >>>> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@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:freesur...@nmr.mgh.**harvard.edu<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 >>>> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.** >>>> edu <gr...@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> >>>> >>>> <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> >>>> >>>> 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/> >>>> >>>> ______________________________**_________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> >>>> <mailto:freesur...@nmr.mgh.**harvard.edu<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. >>>> >>>> >>>> >>> >>> >> >> > -- > 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<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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