Hi Bruce,

Thanks for your answer!

I tried mris_anatomical_stats command, but I met problems: (1) I would like to get the mean intensity ratio of the superior temporal, so I need a label of this region. I first used mri_annotation2label to get lh.superiortemporal.label file.

(2) Then I used mris_anatomical_stats command as following (I saved GM/WM intensity ratio as lh.gm_wm.mgh): mris_anatomical_stats -l label/lh.superiortemporal.label -t subj1/surf/lh.gm_wm.mgh -b -f ./lh.intensity.stats subj1 lh

I didn't get intensity results, rather than mean thickness, area and curvature in this region. I got the same results in above command using "-t lh.thickness" instead of "-t subj1/surf/lh.gm_wm.mgh".

It looks like it didn't read the information of "lh.gm_wm.mgh", even I used "-t subj1/surf/lh.gm_wm.mgh".

I didn't find other appropriate flags which could instead of "-t".

Do you know how to fix this problem?

Thanks for your help!

Regards

Li

________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, December 03, 2012 2:51 PM To: Kong, Li Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Calculatin​g the mean intensity ratio in one specific region

Hi Li

save it as a .mgz volume and use mris_anatomical_stats with the parcellation you want.

cheers Bruce On Mon, 3 Dec 2012, Kong, Li wrote:

Hello everyone,

I got grey matter/ white matter intensity ratio at each vertex across the cortex. I would like to know the mean intensity ratio in one region (ex, superior temporal gyrus).

Anyone knows how to get it?

Thanks in advance!

Li

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

Hi Doug,

Thanks for your idea! It works with mri_segstats.

Regards Li

-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Douglas Greve Gesendet: 03 December 2012 22:35 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Calculatin​g the mean intensity ratio in one specific region

Hi Li, they should not have been identical. The data under the "ThickAvg" column should be the value you want. This and other columns are mislabeled when thickness is not the actual input (eg, GrayVol is meaningless). You might prefer to use mri_segstats, something like

mri_segstats --slabel subject lh lh.superiortemporal.label --i lh.gm_wm.mgh --o gm_wm.sum.dat --excludeid 0

doug

On 12/3/12 10:12 AM, Kong, Li wrote:

Hi Bruce,

Thanks for your answer!

I tried mris_anatomical_stats command, but I met problems: (1) I would like to get the mean intensity ratio of the superior temporal, so I need a label of this region. I first used mri_annotation2label to get lh.superiortemporal.label file.

(2) Then I used mris_anatomical_stats command as following (I saved GM/WM intensity ratio as lh.gm_wm.mgh): mris_anatomical_stats -l label/lh.superiortemporal.label -t subj1/surf/lh.gm_wm.mgh -b -f ./lh.intensity.stats subj1 lh

I didn't get intensity results, rather than mean thickness, area and curvature in this region. I got the same results in above command using "-t lh.thickness" instead of "-t subj1/surf/lh.gm_wm.mgh".

It looks like it didn't read the information of "lh.gm_wm.mgh", even I used "-t subj1/surf/lh.gm_wm.mgh".

I didn't find other appropriate flags which could instead of "-t".

Do you know how to fix this problem?

Thanks for your help!

Regards

Li

---

From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, December 03, 2012 2:51 PM To: Kong, Li Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Calculatin​g the mean intensity ratio in one specific region

Hi Li

save it as a .mgz volume and use mris_anatomical_stats with the parcellation you want.

cheers Bruce On Mon, 3 Dec 2012, Kong, Li wrote:

...

Hello everyone,

I got grey matter/ white matter intensity ratio at each vertex across the cortex. I would like to know the mean intensity ratio in one region (ex, superior temporal gyrus).

Anyone knows how to get it?

Thanks in advance!

Li

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

---

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