External Email - Use Caution
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 <dgr...@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 <dgr...@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 <mj70...@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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