On 11/03/2015 07:03 PM, Jeni Chen wrote: > Thank you Doug. I was actually referring to the following values > (example of my log output below): > > $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ > cwd /Volumes/pathname > cmdline mri_glmfit --y > /Volumes/pathname/lh.Group_abcd.thickness.10.mgh --C > ./pathname/tmp.mri_glmfit-sim-34418/Group-diff_abcd.mtx --C > ./pathname/tmp.mri_glmfit-sim-34418/Group-avg_abcd.mtx --mask > ./pathname/mask.mgh --sim mc-z 5000 1.3 > ./pathname/csd/mc-z.abs.1.3.j001 --sim-sign abs --fwhm 13.034857 > --fsgd ./pathname/y.fsgd dods --label > /Volumes/pathname/lh_abcd_mask.label --surf fsaverage lh white > sysname Darwin > hostname computer.local > machine x86_64 > user jeni > FixVertexAreaFlag = 1 > UseMaskWithSmoothing 1 > fwhm 13.034857 > niters 125.000000 > OneSampleGroupMean 0 > y /Volumes/pathname/lh.Group_abcd.thickness.10.mgh > logyflag 0 > usedti 0 > FSGD ./pathname/y.fsgd > labelmask /Volumes/pathname/lh_abcd_mask.label > maskinv 0 > glmdir (null) > IllCondOK 0 > ReScaleX 1 > DoFFx 0 > Loading y from /Volumes/pathname/lh.Group_abcd.thickness.10.mgh > INFO: gd2mtx_method is dods > Normalized matrix condition is 14.1782 > Matrix condition is 289425 > Found 9260 points in label. > *Found 7440 voxels in mask* > *Reshaping mriglm->mask...* > *search space = 3795.353314* > DOF = 37 > thresh = 1.3, threshadj = 0.99897 > > I do see that it gives information on the number of voxels in the mask > (which is 7440 in the above example). What I was referring to is the > next number "search space = 3795.35..." > Is that the search area? Yes, that is the surface area of the search space. The mri_segstats command should give you the same value as above. If you want to run it, use the mask.mgh that gets created when mri_glmfit is run > > Also in your reply, I see the need to specify the mask.mgh. How do I > specify it if my mask is a label file and not in mgh format? > > Thanks again. > > Jeni > >> On Fri, 30 Oct 2015 08:21 PM Douglas Greve wrote: >> That number is in voxels or vertices. If you want surface area, then use >> mri_segstats something like >>> mri_segstats --i $SUBJECTS_DIR/fsaverage/surf/lh.white.avg.area.mgh >>> --seg glmdir/mask.mgh --id 1 --accumulate --sum sum.dat doug On >>> 10/29/15 5:10 PM, Jeni Chen wrote: > Hello, > > When running the >>> Clusterwise Correction for Multiple Comparisons, I used a > label as >>> a mask to restrict search area. I want to find out the size of that >>> > label, so I guess I can pull that information out from the >>> "mri_glmfit.log", > specifically under 'searchspace'? Also I only >>> see a numerical value there, I > assume it is in mm2? > > Thanks. > >>> > Jeni >
-- 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 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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 . 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.
