Dear Doug,

--sumwf seems to work fine - it gives subjectwise values and values seems of to be of volume:

11262.26605
9294.07182
12673.14610
12601.33416
11141.31917

....

Whenever you get a chance, could you please confirm if --sumwf is the correct flag here?

Thanks.

On Wed, Sep 30, 2020 at 1:04 PM Martin Juneja <mj70481@gmail.com> wrote:

Dear Doug,

Yes, that gives me subjectwise values if I run the following command, but now the output doesn't seem to be the volume values, it gives very small subjectwise values as following:

mri_segstats --seg lh.HC_GAD.vol.glmdir/p_bin.mgz --excludeid 0 --i lh.HC_GAD.vol.10.mgh --accumulate --avgwf volumesum1.table

Output:

1.49360
1.71227
1.84950
1.58922
1.98355
1.49314
1.37157
1.77108
1.87064
2.08438
1.87076
1.61026
2.42607
1.69756
1.65158
1.61560
On Wed, Sep 30, 2020 at 12:58 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
Use the --avgwf output.table instead of --sum

On 9/30/2020 1:48 PM, Martin Juneja wrote:
External Email - Use Caution

Dear Doug,

Thanks for your response. I created a binary mask and ran the following command, but the output gives me only one value of volume as follows. I was wondering how I can extract the values for each subject.

mri_segstats --seg lh.HC_GAD.vol.glmdir/p_bin.mgz --excludeid 0 --i lh.HC_GAD.vol.10.mgh --accumulate --sum volumesum.dat

.....

.....

# ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range
1 1 6126 6126.0 Seg0001 11262.2666 0.5353 0.9159 3.4016 2.4857
On Wed, Sep 30, 2020 at 9:17 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
If you have a binary mask or cluster mask, you can use mri_segstats, like
mri_segstats --seg binary-or-clustermask.mgz --excludeid 0 --i volumestack.mgz --accumulate --sum volumesum.dat
where volumestack.mgz is a stack of the subjects volume (eg, created by mris_preproc)

On 9/29/2020 1:32 PM, Martin Juneja wrote:
External Email - Use Caution

Dear Doug and FreeSurfer team,

Any help with this on an urgent basis would be really appreciated. Sorry for being a little impatient :(.

Thank you so much !

---------- Forwarded message ---------
From: Martin Juneja <mj70481@gmail.com>
Date: Mon, Sep 28, 2020 at 5:42 PM
Subject: Extraction of subject-wise values after permutation test !
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>

Hello everyone,

I have significant group differences in volume (controls > patients) for one of the clusters (say C1) - calculated after permutation test using PALM, which gives me following outputs:

*_clustere_tstat_fwep.mgz (this is significant at p < 0.05, number of voxels = 1105)
*_clustere_tstat.mgz
*_dpv_tstat_fwep.mgz
*_dpv_tstat_uncp.mgz
*_dpv_tstat.mgz

I was wondering if there is a way to calculate volume values of C1 for each subject (i.e., controls and patients).

Thanks.
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