Re: [Freesurfer] matrix is ill-conditioned or badly scaled

NaN will not work for this. You can't do incomplete designs with an FSGD. You can create your own design matrix and pass it with --X, otherwise you'll have to exclude those subjects or put some reasonable (eg, imputed) value On 1/12/2021 6:35 PM, Julie Ottoy wrote: External Email - Use

[Freesurfer] matrix is ill-conditioned or badly scaled

External Email - Use Caution Hi freesurfer experts, I am trying to run a GLM fit between cortical thickness and some other continuous marker. My cortical thickness were stacked before using the mris_preproc and surf2surf commands. I have an FSGD file with the same subjects as

Re: [Freesurfer] Matrix is ill-conditioned or badly scaled

The problem is that some of your groups are very small, eg, groups 2 and 4 only have 3 subjects. The way you have it set up, there are four parameters (offset and 3 slopes) for each group. Thus, you are running out of DOFs for those two groups (and not so much better on some of the others).

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

External Email - Use Caution Hi Doug, I realized this error a couple of days ago and now it works. Thank you, Arsenije ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

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

Your FSGD file is incorrect in several ways. Under "variables" you have "Sex" and list "Male" and "Female". The variables must be numbers, not strings. The variables should also represent continuous quantities, not categories. To handle sex, you should have a total of 6 categories, the 3 that

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

External Email - Use Caution Hi, I am still struggling to examine differences in thickness using the command line stream for my two groups after controlling for age and sex. I get the following error when running the command line: ERROR: matrix is ill-conditioned or badly

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] 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] 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

Did you see the line "If you seek help with this problem, make sure to send:" and then it lists some things to send On 2/25/19 2:13 PM, Arsenije Subotic wrote: > > External Email - Use Caution > > Dear experts, > > I have recently tried to use the command line to examine thickness >

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

External Email - Use Caution 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 following error : ERROR: matrix is ill-conditioned or badly scaled, condno =

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

You have commas (ie, ",") instead of decimal points (ie, ".") in your fsgd file. Try replacing them and see if that works On 03/16/2017 08:59 AM, teodora petrova wrote: > Hello, > > I am trying to use the glm_fit to correlate a continuous variable > (index) with cortical thickness, when

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

Hello, I am trying to use the glm_fit to correlate a continuous variable (index) with cortical thickness, when controlling for age, education, and cognition (MMSE) (all continuous variables). However, I get the following error: ERROR: matrix is ill-conditioned

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

Thank you for catching this. Really appreciate your help. - Arkadiiy ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person

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

You have no HDFemales so the 2nd column is 0. On 6/21/16 7:40 PM, Arkadiy Maksimovskiy wrote: Hello, Hello, I am getting the following error: ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 Command line: mri_glmfit --y

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

Hello, Hello, I am getting the following error: ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 Command line: mri_glmfit --y lh.BD_SD.thickness.10B.mgh --fsgd FSGD_Collapsed_Across_Smokers_demeaned.fsgd dods --C BDvsSD1.mtx --surf fsaverage

Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 27492.1

Try multiplying the covariate by 100 (after subtracting the mean). On 2/5/16 8:28 AM, Nabin Koirala wrote: I did that but it still does not work, it is almost the same error except the condno is now 15521.8 before it was 27492.1, though I am not sure if that tells something about the error.

Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 27492.1

I did that but it still does not work, it is almost the same error except the condno is now 15521.8 before it was 27492.1, though I am not sure if that tells something about the error. Could it be something else ? Thank you. Regards, Nabin On Thu, Feb 4, 2016 at 5:59 PM, Douglas Greve

Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 27492.1

I'm not sure what the difference is. Compute the mean of the 2nd column, then subtract that number from the values in the 2nd column. doug On 2/2/16 7:30 AM, Nabin Koirala wrote: Thank you for your response . Sorry but for my understanding, should i substract the mean from the data (demean) or

Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 27492.1

Thank you for your response . Sorry but for my understanding, should i substract the mean from the data (demean) or you mean to remove the value which is equal to the mean ? Thank you. Regards, Nabin On Mon, Feb 1, 2016 at 5:21 PM, Douglas N Greve wrote: > Try

Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 27492.1

Try removing the mean from your covariate On 01/30/2016 01:31 PM, Nabin Koirala wrote: > Dear Freesurfer forum, > > 'I am trying to run qdec analysis for a group of subjects to see if > correlation exists but I am getting this error only for this > particular set of data but could not figure

[Freesurfer] matrix is ill-conditioned or badly scaled, condno = 27492.1

Dear Freesurfer forum, 'I am trying to run qdec analysis for a group of subjects to see if correlation exists but I am getting this error only for this particular set of data but could not figure out what is exactly wrong with it. Your suggestion would be greatly appreciated. Following is the

Re: [Freesurfer] matrix is ill-conditioned or badly scaled

Hi Doug Thanks a lot for your answer Cheers Jürgen --- - Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97

Re: [Freesurfer] matrix is ill-conditioned or badly scaled

Looks like your fsgd file was created under a windows machine or old macos, try converting the fsgd like this cat old.fsgd | sed 's/\\r/\\n/g' new.fsgd On 08/22/2014 02:51 AM, Jürgen Hänggi wrote: Dear FS experts We run mri_glmfit and encountered the following error: INFO: