[Freesurfer] model for pair-T test
Hello, group, Could anybody tell me how to do the pair T test and the repeat measurement F test? I will really appreciate if you can share the steps and GLM of the tests. I am using the old freesurfer group analysis. Thank you, very much, Xin Wang ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] model for pair-T test
Can you use the --paired-diff to mris_preproc? Wang, Xin wrote: Hello, group, Could anybody tell me how to do the pair T test and the repeat measurement F test? I will really appreciate if you can share the steps and GLM of the tests. I am using the old freesurfer group analysis. Thank you, very much, Xin Wang ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] model for pair-T test
Please give me more detailed explanations of how to run mris_preproc --paired-diff or (--paired-diff-norm)? and how to setup the GLM after run this commend? I could not find needed information on the website. Thank you very much. Xin From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Fri 10/5/2007 5:20 PM To: Wang, Xin Cc: freesurfer Subject: Re: [Freesurfer] model for pair-T test Can you use the --paired-diff to mris_preproc? Wang, Xin wrote: Hello, group, Could anybody tell me how to do the pair T test and the repeat measurement F test? I will really appreciate if you can share the steps and GLM of the tests. I am using the old freesurfer group analysis. Thank you, very much, Xin Wang ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] model for pair-T test
The --paired-diff options just take the difference between adjacently specfied inputs. You then set up your design matrix or FSGD file and then run mri_glmfit. The --help for mri_glmfit has a lot of info about the glm analysis. If you just want to test whether the difference is 0, you can use the --osgm flag (one-sample group mean). doug Wang, Xin wrote: Please give me more detailed explanations of how to run mris_preproc --paired-diff or (--paired-diff-norm)? and how to setup the GLM after run this commend? I could not find needed information on the website. Thank you very much. Xin From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Fri 10/5/2007 5:20 PM To: Wang, Xin Cc: freesurfer Subject: Re: [Freesurfer] model for pair-T test Can you use the --paired-diff to mris_preproc? Wang, Xin wrote: Hello, group, Could anybody tell me how to do the pair T test and the repeat measurement F test? I will really appreciate if you can share the steps and GLM of the tests. I am using the old freesurfer group analysis. Thank you, very much, Xin Wang ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] model for pair-T test
Hello, Doug, I ran into an error when I ran mri_glmfit after I finished mris_preproc --paired-diff. ERROR: dimension mismatch between y and x. y has 5 inputs, x has 10 inputs. I think it is because the mris_preproc -paired-diff generated 5 inputs of difference within 5 pairs, but my FSGD file still has 10 images. In addition, I do not want to include age as regressor. but if I deleted the age column, there is no variable. I attach my FSGD file. Please tell me how to modify the FSGD file. Thank you, Xin Wang From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Fri 10/12/2007 4:21 PM To: Wang, Xin Cc: freesurfer Subject: Re: [Freesurfer] model for pair-T test The --paired-diff options just take the difference between adjacently specfied inputs. You then set up your design matrix or FSGD file and then run mri_glmfit. The --help for mri_glmfit has a lot of info about the glm analysis. If you just want to test whether the difference is 0, you can use the --osgm flag (one-sample group mean). doug Wang, Xin wrote: Please give me more detailed explanations of how to run mris_preproc --paired-diff or (--paired-diff-norm)? and how to setup the GLM after run this commend? I could not find needed information on the website. Thank you very much. Xin From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Fri 10/5/2007 5:20 PM To: Wang, Xin Cc: freesurfer Subject: Re: [Freesurfer] model for pair-T test Can you use the --paired-diff to mris_preproc? Wang, Xin wrote: Hello, group, Could anybody tell me how to do the pair T test and the repeat measurement F test? I will really appreciate if you can share the steps and GLM of the tests. I am using the old freesurfer group analysis. Thank you, very much, Xin Wang ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting GroupDescriptorFile 1 Title back to back no rp Class first Class second Variables age Input APN01R650_4 first 23 Input APN01R650_5 second 23 Input APN02G650_4 first 36 Input APN02G650_5 second 36 Input APN03L650_3 first 24 Input APN03L650_4 second 24 Input APN04E650_2 first 50 Input APN04E650_3 second 50 Input APN05T650_2 first 23 Input APN05T650_3 second 23 DefaultVariable age ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] model for pair-T test
yes, after the paired diff, you should create a new fsgd file that has only one entry per subject (it does not matter which one). You do not have to have a variable. Wang, Xin wrote: Hello, Doug, I ran into an error when I ran mri_glmfit after I finished mris_preproc --paired-diff. ERROR: dimension mismatch between y and x. y has 5 inputs, x has 10 inputs. I think it is because the mris_preproc -paired-diff generated 5 inputs of difference within 5 pairs, but my FSGD file still has 10 images. In addition, I do not want to include age as regressor. but if I deleted the age column, there is no variable. I attach my FSGD file. Please tell me how to modify the FSGD file. Thank you, Xin Wang From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Fri 10/12/2007 4:21 PM To: Wang, Xin Cc: freesurfer Subject: Re: [Freesurfer] model for pair-T test The --paired-diff options just take the difference between adjacently specfied inputs. You then set up your design matrix or FSGD file and then run mri_glmfit. The --help for mri_glmfit has a lot of info about the glm analysis. If you just want to test whether the difference is 0, you can use the --osgm flag (one-sample group mean). doug Wang, Xin wrote: Please give me more detailed explanations of how to run mris_preproc --paired-diff or (--paired-diff-norm)? and how to setup the GLM after run this commend? I could not find needed information on the website. Thank you very much. Xin From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Fri 10/5/2007 5:20 PM To: Wang, Xin Cc: freesurfer Subject: Re: [Freesurfer] model for pair-T test Can you use the --paired-diff to mris_preproc? Wang, Xin wrote: Hello, group, Could anybody tell me how to do the pair T test and the repeat measurement F test? I will really appreciate if you can share the steps and GLM of the tests. I am using the old freesurfer group analysis. Thank you, very much, Xin Wang ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting GroupDescriptorFile 1 Title back to back no rp Class first Class second Variables age Input APN01R650_4 first 23 Input APN01R650_5 second 23 Input APN02G650_4 first 36 Input APN02G650_5 second 36 Input APN03L650_3 first 24 Input APN03L650_4 second 24 Input APN04E650_2 first 50 Input APN04E650_3 second 50 Input APN05T650_2 first 23 Input APN05T650_3 second 23 DefaultVariable age -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
