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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
what version of FS are you using? there should be a file with "summary" in the name. Also, try looking at the help with mri_glmfit-sim --help doug
On 02/21/2014 11:39 PM, charujing123 wrote:
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 clusterwith 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
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
Sorry, the summary file is not what you want. Can you send a list of the files in the folder? doug
On 02/24/2014 11:26 AM, Douglas N Greve wrote:
what version of FS are you using? there should be a file with "summary" in the name. Also, try looking at the help with mri_glmfit-sim --help doug
On 02/21/2014 11:39 PM, charujing123 wrote:
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 clusterwith 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
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
freesurfer@nmr.mgh.harvard.edu
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charujing123 -
Douglas N Greve