Hidoug, Thanks doug. For 1st question,I want to reduce the search space of vertex-wise analysis to a cluster. For 2nd question, i try freeview as tksurfer cannot work. However this website cannot be logged in:http://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewTools/RoiEdit. Thanks. All the best. Rujing Zha

2014-02-26

charujing123

发件人：Douglas Greve greve@nmr.mgh.harvard.edu 发送时间：2014-02-25 23:46 主题：Re: [Freesurfer] questions about ROI analysis 收件人："freesurfer"freesurfer@nmr.mgh.harvard.edu 抄送：

On 2/25/14 10:09 AM, Rujing Zha wrote:

Hi FS experts and others, I have done two group thickness difference analysis based on whole brain. Now I want to do correlation analysis between specific ROI thickness and behavior score. I searched roi in the FS website, but I cannot distinguish the volume ROI and surface ROI very clearly. So I have some questions as below: 1,As I get some clusters in the two group t-test,I want to use one of these clusters to correlate thickness with behavior score. How to generate this mask and how to use this mask in the mri_glmfit and mri_glmfit-sim? Do you mean you want to reduce the search space of a vertex-wise analysis to a cluster or that you want to compute the mean thickness within the cluster and correlate with your behavioral score?

2,If I want to draw ROI manually or set ROI according previous studies, how to create this ROI mask. tksurfer can draw a label (as can freeview I think)

Any detailed information will be highly appreaciated. Thanks. All the best. Rujing Zha

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Thanks doug, All the best. Rujing Zha

2014-02-27

charujing123

发件人：Douglas N Greve greve@nmr.mgh.harvard.edu 发送时间：2014-02-27 01:49 主题：Re: [Freesurfer] questions about ROI analysis 收件人："freesurfer"freesurfer@nmr.mgh.harvard.edu 抄送：

On 02/25/2014 08:34 PM, charujing123 wrote:

Hidoug, Thanks doug. For 1st question,I want to reduce the search space of vertex-wise analysis to a cluster.

Extract the cluster that you want from the ocn to create a mask, eg, to get cluster2 mri_binarize --i ocn.mgh --match 2 --o cluster2.mgh The run mri_glmfit with --mask cluster2.mgh Then run mri_glmfit-sim with simulation

For 2nd question, i try freeview as tksurfer cannot work. However this website cannot be logged in:http://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewTools/RoiEdit.

try http://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide

Thanks. All the best. Rujing Zha 2014-02-26

---

charujing123

*发件人：*Douglas Greve greve@nmr.mgh.harvard.edu *发送时间：*2014-02-25 23:46 *主题：*Re: [Freesurfer] questions about ROI analysis *收件人：*"freesurfer"freesurfer@nmr.mgh.harvard.edu *抄送：*

On 2/25/14 10:09 AM, Rujing Zha wrote:

...

Hi FS experts and others, I have done two group thickness difference analysis based on whole brain. Now I want to do correlation analysis between specific ROI thickness and behavior score. I searched roi in the FS website, but I cannot distinguish the volume ROI and surface ROI very clearly. So I have some questions as below: 1,As I get some clusters in the two group t-test,I want to use one of these clusters to correlate thickness with behavior score. How to generate this mask and how to use this mask in the mri_glmfit and mri_glmfit-sim?

Do you mean you want to reduce the search space of a vertex-wise analysis to a cluster or that you want to compute the mean thickness within the cluster and correlate with your behavioral score?

...

2,If I want to draw ROI manually or set ROI according previous studies, how to create this ROI mask.

tksurfer can draw a label (as can freeview I think)

...

Any detailed information will be highly appreaciated. Thanks. All the best. Rujing Zha

---

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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