Re: [Freesurfer] Fwd: Extraction of subject-wise values after permutation test !

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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:

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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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