Got it. Thanks for the prompt answer! By the way, I tried mri_segstats with --accumulate flag, but it says option '--accumulate' is unknown. I don't seem to find it when I looked up mri_segstas --help either.
On Tue, Jun 11, 2013 at 5:05 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > > 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 -- >> 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 <http://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 >> <mailto:gr...@nmr.mgh.harvard.**edu<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> >> > >> <mailto:gr...@nmr.mgh.harvard.**edu <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%2081837%20%2081837> >> >> <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> >> > >> <mailto:gr...@nmr.mgh.harvard.**edu<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> >> > >> >> <mailto:gr...@nmr.mgh.harvard.**edu<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> >> > >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<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> >> > >> >> <mailto:gr...@nmr.mgh.harvard.**edu<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> <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>> >> <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> >> > >> <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> >> > >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<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 >> <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/> >> >> >> > -- > 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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