Re: [Freesurfer] Second order (square) link function for GLM

just deman after you do the square root On 3/1/19 3:49 AM, Abhinav Yadav wrote: External Email - Use Caution Hi Douglas, Thanks. But I want to see the square root of the age because I am assuming that the brain feature (cortical thickness) is varying in a square fashion. Do I

Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08

External Email - Use Caution Hi Doug, Thank you for your reply. My command was: mri_glmfit.bin --y CAA_CTRL_RH.thickness.10.mgh --fsgd CAA_CTRL_RH_Age_Sex.fsgd --C Contrasts/CAA-CTRL_Age_Sex.mtx --surf fsaverage rh --cortex --glmdir CAA_CTRL_RH_Age_Sex_Unix.glmdir My FSGD

Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08

sorry, can you also include the previous emails so I know what the context is? On 3/1/19 1:02 PM, Arsenije Subotic wrote: External Email - Use Caution Hi Doug, Thank you for your reply. My command was: mri_glmfit.bin --y CAA_CTRL_RH.thickness.10.mgh --fsgd CAA_CTRL_RH_Age_Sex.fsgd

Re: [Freesurfer] projfrac question

Yes, I found it. I should mention that, this log file is the result of today's preprocessing (-projfrac 0.2) which I did in a separate folder, with all the previous preprocessing files being deleted. As you see the -projfrac is still 0.5 ! Fri Mar 1 11:32:16 EST 2019 mri_vol2surf --mov

Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08

External Email - Use Caution Hi Doug, This is the bulk of the text I wrote initially in my first email: Dear experts, I have recently tried to use the command line to examine thickness differences between two groups after controlling for the effects of age and sex. I get the

Re: [Freesurfer] dt_recon field map for eddy correct

I don't know, probably a better question for the FSL group On 3/1/19 8:57 AM, Daniel Callow wrote: External Email - Use Caution Hi Doug, I was looking at the dt_recon code and was wondering if it would be possible to incorporate a field map into the eddy_correct portion? I tried to

Re: [Freesurfer] Second order (square) link function for GLM

if they are negative, it seems like a square root model is not appropriate On 3/1/19 11:03 AM, Abhinav Yadav wrote: External Email - Use Caution In my case the behavioural values are already positive and negative. What about that. On Fri, 1 Mar 2019, 23:58 Greve, Douglas N.,Ph.D.,

Re: [Freesurfer] Second order (square) link function for GLM

External Email - Use Caution In my case the behavioural values are already positive and negative. What about that. On Fri, 1 Mar 2019, 23:58 Greve, Douglas N.,Ph.D., wrote: > just deman after you do the square root > > On 3/1/19 3:49 AM, Abhinav Yadav wrote: > >

Re: [Freesurfer] projfrac question

that is part of the bbregister command. Can you find the commands related to mri_vol2surf? On 2/28/19 3:51 PM, Nasiriavanaki, Zahra wrote: I did not find mri_vol2surf. Below is part of a log file, as you see -projrfac has changed to 0.5 but not to 0.2. mri_segreg --mov

Re: [Freesurfer] Second order (square) link function for GLM

External Email - Use Caution Hi Douglas, Thanks. But I want to see the square root of the age because I am assuming that the brain feature (cortical thickness) is varying in a square fashion. Do I have to put square root values? If yes then, how can I put negative square

[Freesurfer] dt_recon field map for eddy correct

External Email - Use Caution Hi Doug, I was looking at the dt_recon code and was wondering if it would be possible to incorporate a field map into the eddy_correct portion? I tried to test it on one subject and tried to add --field=$pathtofieldmap to the eddy_correct command