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?
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
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
On Nov 3, 2015, at 8:01 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Found 9260 points in label. *Found 7440 voxels in mask* *Reshaping mriglm->mask...* *search space = 3795.
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
Thanks! And that's in mm^2, correct?
Jeni
yes, mm2
On 11/3/15 9:06 PM, Chen Jen-I. wrote:
On Nov 3, 2015, at 8:01 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Found 9260 points in label. *Found 7440 voxels in mask* *Reshaping mriglm->mask...* *search space = 3795.
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
Thanks! And that's in mm^2, correct?
Jeni
freesurfer@nmr.mgh.harvard.edu
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Chen Jen-I. -
Douglas Greve -
Douglas N Greve
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Jeni Chen