External Email - Use Caution Thank you Douglas! If I apply my transform to both the healthy controls and the patient, I guess I would lose the convenience of using mri_glmfit, which eventually loses the convenience of using mri-glmfit-sim (I don't care not using mri_glmfit, but I want to use mri_glmfit-sim to do multiple comparisons correction). That is because mri_glmfit uses the prepared output from mris_preproc, which I have no control over to use the transformed subject. The only way I can circumvent this is to use my transformed thickness file to overwrite the FS calculated thickness file, but that is what I am hesitant to do. If you have good suggestions regarding this, please let me know. Thanks! Xiao
On Mon, May 11, 2020 at 12:25 PM Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > I guess you could apply your transform to both the healthy controls and to > your patient, can then create an FSGD file with two classes as before but > no continuous variable. Then just have a contrast that computes the diff > between the patient and the mean of the controls. > > On 5/8/2020 11:49 AM, Xiaojiang Yang wrote: > > External Email - Use Caution > > Hi Douglas, > > > > Could you please reply my last email (sent to > freesurfer@nmr.mgh.harvard.edu) regarding my question about the weighted > age? I am eager to listen to your answer/opinion to my question. For your > convenience, I also include the whole email chain below this email. > > > > Thank you very much! > > > > Sincerely, > > Xiao > > > > > > <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from > > :%22Douglas+N.+Greve%22> Douglas N. Greve > > <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date > > :20200507> Thu, 07 May 2020 14:56:08 -0700 > > > > sorry, please include the previous email chain so that I know what you are > > referring to > > > > > > > > > > On 5/7/2020 5:33 PM, Xiaojiang Yang wrote: > > External Email - Use Caution > > Douglas, > > > > Just as I mentioned in the initial email, subjects in the healthy group have > > different ages. Because average cortical thickness is believed to be > > declined as the age gets older, I want to "normalize" the group by > > multiplying each subject's thickness with an age-dependent scalar > > (pre-calculated constant). Suppose I take age 30 as the "standard" age, then > > subjects with ages greater than 30 will have scalars greater than 1 (depend > > on age); subjects with ages smaller than 30 will have scalars less than 1. > > In this way, all subjects in the group looks like to be at the same age > > (30). > > > > > > Of course, I also suspect that there is no need to do the above mentioned > > normalization if I use mri_glmfit. But my initial intention was using > > non-linear scalars, and mri_glmft can only use linear fit. Please give me > > your opinion. Thank you! > > > > Xiao > > > > > > <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from > > :%22Douglas+N.+Greve%22> Douglas N. Greve > > <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date > > :20200507> Thu, 07 May 2020 14:06:27 -0700 > > > > I don't know what weight is. Can you elaborate? > > On 5/7/2020 4:54 PM, Xiaojiang Yang wrote: > > External Email - Use Caution > > Hi Douglas, > > > > Thank you very much! Could you please help me with more detailed > > information? > > > > > > 1)Should I use "Variables age" or "Variables age weight" in the fsgd file? > > If I can use either of them, which one is better? > > > > I don't know what weight is. Can you elaborate? > > > > 2)For the contrast file, the content "1 -1 0" you mentioned, it corresponds > > to the "Variables age" fsgd file, correct? > > > > Yes > > > > 3)If I use the "Variables age weight" fsgd file, what will be the content of > > the contrast file? Is it "1 -1 0 0"? > > > > Yes > > Thank you again! > > Xiao > > > > > > > > <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from > > :%22Douglas+N.+Greve%22> Douglas N. Greve > > <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date > > :20200507> Thu, 07 May 2020 11:55:27 -0700 > > > > I think it will work properly if you use the raw data as input and create an > > FSGD file with two classes: (1) the individual subject and (2) healthy > > subjects. Also include age as a covariate. Use DOSS instead of DODS. Then > > set your contrast to be 1 -1 0 and run mri_glmfit. I think that should > > properly account for age. > > > > > > > > > > > > On 5/7/2020 2:44 PM, Xiaojiang Yang wrote: > > > > > > External Email - Use Caution > > > > > > Dear FS experts, > > > > > > I have a group of healthy subjects. Given a new individual subject, I want > > to compare its cortical thickness to the healthy group so that I can find > > where the thickness is abnormal (thickening or thinning). > > > > > > I use fsaverage as the template subject to calculate mean and std of the > > healthy group. Since subjects in the healthy group have different ages, I do > > a "normalization" process to all the subjects in the group BEFORE > > calculating the mean and std. Thus the normalized healthy group can be > > regarded as all subjects having the same "standard" age. The normalization > > process is just multiplying some pre-obtained scale (varied by age, but not > > linearly ) to the file *?h.thickness.fwhm0.fsaverage.mgh* of each subject > > that are already calculated by "recon-all --qcache" command. So the mean and > > std of the group are actually weighted in the sense of Freesurfer's > > recon-all results. > > > > > > My questions are: > > > > > > 1)If I do vertex-wise t-tests by simply comparing individual subject's > > thickness to the group using mris_calc but WITHOUT using mri_glmfit, can I > > still use mri_glmfit-sim to do multiple comparisons correction? If yes, how? > > > > > > 2)If the answer is no for the above question, how should I use mris_glmft to > > implement my above thoughts so that I can use use mri_glmfit-sim? > > Specifically, how can I use the weighted mean for the group? > > > > > > 3)Take a step back, if I consider the weight is linearly correlated with the > > age, how to design the fsdg and contrast file? > > > > > > Thank you very much! > > > > > > Xiao > > > > > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. >
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