$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?

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