Use the --avgwf output.table instead of --sum

On 9/30/2020 1:48 PM, Martin Juneja wrote:

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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:

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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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