Thank you for your reply. The values of mri_segstats output text file (lateral.txt) are high. I attached it to this email.
mri_segstats --i $all_subjects/$subj/rest/009/fmcpr.sdf.sm5.mni305.2mm.nii.gz --seg $SUBJECTS_DIR/$subj/mri/reg.lh.HBT.mgz --id 7001 --avgwf lateral.txt ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu> Sent: Thursday, April 11, 2019 4:19:00 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_segstats The value of what is too high? On 4/11/19 4:07 PM, Nasiriavanaki, Zahra wrote: > > Hi > > > I have not got the answer to my question yet, and I appreciate if you > could please let me know what you think about it. > > > Thanks > > Mona > > ------------------------------------------------------------------------ > *From:* Nasiriavanaki, Zahra > *Sent:* Tuesday, April 9, 2019 5:55:58 PM > *To:* Freesurfer support list > *Subject:* mri_segstats > > Dear Freesurferers > > > I was trying to do a connectivity analysis using subnuclei of Amygdala. > > I had an Amygdala segmentation file (reg.lh.HBT.mgz for letf > Amygdala) and I tried to use that in mri_segstats to extract the > timeseries and then use it as a seed in my analysis. However when I > looked at the results, the values are too high (around 800). Could you > please let me know what I'm doing wrong? > > P.S: the segmentation was basically done in MNI152-1mm and I moved it > to MNI305-2mm by mri_vol2vol. > > mri_vol2vol --mov MNI152template/MNI152_1/mri/reg.lh.HBT.mgz --targ > $SUBJECTS_DIR/fsaverage/mri.2mm/mni305.cor.mgz --o > $SUBJECTS_DIR/$subj/mri/reg.lh.HBT.mgz --interp nearest --regheade > > mri_segstats --i > $all_subjects/$subj/rest/009/fmcpr.sdf.sm5.mni305.2mm.nii.gz --seg > $SUBJECTS_DIR/$subj/mri/reg.lh.HBT.mgz --id 7001 --avgwf lateral.txt > > > Thanks a lot > > MOna > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://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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