External Email - Use Caution 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 <mj70...@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 <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. >>> >>> _______________________________________________ >>> Freesurfer mailing >>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >
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