Re: [Freesurfer] Compare individual to a group

Did you try specifying your xformed file as the argument to --cached-in ? If that does not work, then transform the thickness in the native surface,then run mris_preproc, then smooth with mris_fwhm On 5/12/2020 11:37 PM, Xiaojiang Yang wrote: External Email - Use Caution Hi Douglas,

Re: [Freesurfer] Compare individual to a group

External Email - Use Caution Hi Douglas, I have tried to follow your suggestion to use the transformed thickness file like this: mris_preproc --fsgd xxx.fsgd \ --meas $meas.fwhm$smoothing.xformed.mgz \ --target fsa

Re: [Freesurfer] Compare individual to a group

Just call your thickness file some other name, eg, lh.xformed.thickness.mgz, the just specify --meas xformed.thickness.mgz On 5/11/2020 3:52 PM, Xiaojiang Yang wrote: External Email - Use Caution Thank you Douglas! If I apply my transform to both the healthy controls and the patient,

Re: [Freesurfer] Compare individual to a group

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 w

Re: [Freesurfer] Compare individual to a group

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,

Re: [Freesurfer] Compare individual to a group

External Email - Use Caution Hi Douglas, Sorry I didn't find an easy way to include previous email chain. Now I just copied all of them below, so that it's easy to follow. Thanks, Xiao

Re: [Freesurfer] Compare individual to a group

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 corti

Re: [Freesurfer] Compare individual to a group

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 thi

Re: [Freesurfer] Compare individual to a group

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 fi

Re: [Freesurfer] Compare individual to a group

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? 2) For the contrast

Re: [Freesurfer] Compare individual to a group

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 pr

[Freesurfer] Compare individual to a group

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 tem