Hi FS experts and others, I completed the mri_annotation2label and mri_label2label(which used mask created from the mri_binarize), but the result is the same as that without mask.Here are my codes: ==================================================================================== mri_binarize --i *.ocn.mgh --match 1 --o cluster1.mgh mri_annotation2label --subject fsaverage --hemi rh --outdir $SUBJECTS_DIR/fsaverage/label mri_label2label --srclabel $SUBJECTS_DIR/fsaverage/label/rh.superiofrontal.label --srcsubject fsaverage --trgsubject test --regmethod volume --srcmask cluster1.mgh 1 bfloat ==================================================================================== Last step used the mask, but its result is just tha same as that without mask. I also checked the mask file which doesnot have any problem. Thanks. All the best. Rujing Zha
-------- 转发邮件信息 -------- 发件人：charujing123 charujing123@163.com 发送日期：2014-02-27 09:46:23 收件人："freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu 主题：Re: Re: [Freesurfer] questions about ROI analysis
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
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