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

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*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

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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

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*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@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

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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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@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

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*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@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

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