Hi doug and others,

Creating the something.y.ocn.dat,I find it can only creating an average thickness for one cluster. When my numbers of clusters in *sig.cluster.summary exceeding 1,then it cannot generate the something.y.ocn.dat,and error will be exported in the window:memory corruption.

I know how to set the threshold, that is to say p<threshod value. So I want to know how to set p>0.1or some other value to get only one cluster average thickness.

Thanks.

ALL the best.

Rujing Zha

2014-02-24

charujing123

发件人："charujing123"<charujing123@163.com>

发送时间：2014-02-22 12:39

主题：[Freesurfer] Fw: Re: extracting mean thickness from specific cluster

收件人："freesurfer@nmr.mgh.harvard.edu"<freesurfer@nmr.mgh.harvard.edu>

抄送：

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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