Hi doug, I tried to generate the mean thickness of the cluster in uncorrected p value<0.005 for each subject by this command "mri_glmfit-sim --glmdir lh.score.dir --cwp 1 --cache 2.3 neg". It generates some files named with suffix ".pdf.dat,cluster.mgh,cluster.summary,masked.mgh,ocn.annot,ocn.mgh,voxel.mgh". I cannot find a file that can tell me the mean thickness for each subject. Did I miss something? Thanks. All the best. Rujing Zha
2014-02-22
charujing123
发件人："charujing123"charujing123@163.com 发送时间：2014-02-22 10:08 主题：Re: [Freesurfer] extracting mean thickness from specific cluster 收件人："freesurfer@nmr.mgh.harvard.edu"freesurfer@nmr.mgh.harvard.edu 抄送：
Hi doug and others, Thanks doug. For 1st question:I find that file. However not all has that file.May I generate it manually? Thanks doug. All the best. Rujing Zha
2014-02-22
charujing123
发件人：Douglas Greve greve@nmr.mgh.harvard.edu 发送时间：2014-02-21 23:46 主题：Re: [Freesurfer] extracting mean thickness from specific cluster 收件人："freesurfer"freesurfer@nmr.mgh.harvard.edu 抄送：
On 2/21/14 10:04 AM, charujing123 wrote:
Hi all, I finished the mri_glmfit-sim, and got some clusters in the cluster summary. 1,I want to know how to extract mean thickness for each subject in this cluster?
There should already be a file there called something like something.y.ocn.dat. This will have a row for each subject and a column for each cluster. The value will be the mean for that subject inside that cluster.
2,If I want to extract mean thickness of each subject according to a uncorrected p value, i.e. 0.005, what should I do to perform it?
What do you mean? Over all vertices that survive? Or for each all cluster with a cluster-forming threshold of .005? If the latter, you can run mri_glmfit-sim with --cwp 1 --cache 2.3 abs
Thanks. All the best. Rujing Zha
2014-02-21
charujing123
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