Following my previous question, I have one more question and I appreciate if you could please reply whenever you had time.
I extracted time series from a single resting state run using mri_segstats and compared it to the time series extracted from the same run using (fcseed-config & fcseed-sess). The outputs are very different from each other. I'm wondering why they are different and which one I should use as a seed in the connectivity analysis? mri_segstats --i $subj/rest/009/fmcpr.siemens.sm5.mni305.2mm.nii.gz --seg SUBJECTS_DIR/$subj/mri/reg.lh.HBT2.mgz --id 7001 --avgwf-remove-mean --avgwf lh.lateral.txt fcseed-config -segid 7001 -seg SUBJECTS_DIR/$subj/mri/reg.lh.HBT2.mgz -fcname lh.lateral.dat -fsd rest -rlf restruns -mean -cfg lh.lateral.config -overwrite fcseed-sess -s $subj -d . -cfg lh.lateral.config Thanks Mona ________________________________ From: Nasiriavanaki, Zahra Sent: Thursday, April 11, 2019 4:52:49 PM To: Freesurfer support list Subject: Re: [Freesurfer] mri_segstats Thank you so very much. Yes, the values look normal now. Mona ________________________________ 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 4:33:12 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_segstats You probably need to remove the mean. Add --avgwf-remove-mean to the command line On 4/11/19 4:29 PM, Nasiriavanaki, Zahra wrote: > > Thank you for your reply. > > The values of mri_segstatsoutput 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 Info Page - Harvard University<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> mail.nmr.mgh.harvard.edu To see the collection of prior postings to the list, visit the Freesurfer Archives.. A searchable archive which of messages PRIOR to March 2004 is at this site A searchable archive which includes messages AFTER March 2004 is at this site. Using Freesurfer > > > _______________________________________________ > 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 _______________________________________________ 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
