Dear free surfer developers,
When I try to run the mri_glmfit free surfer does not seem to recognise my FSGD file. I believe it has something to do with the underlying languages, since it appears to occur both when I create a plain txt file or when I adjust the tutorials gender_age.fsgd and adjust the values of the covariates. I have tried tons of things to fix the problem, but i can't seem to figure it out... Do you by any chance have an idea on how I can fix this?
error (in bash): ERROR: matrix is ill-conditioned or badly scaled, condno = 15250.9 command line: mri_glmfit --y lh.CB10.thickness.20.mgh --fsgd doesnotworkretestCB10.fsgd doss --C con-hem.mtx --surf fsaverage lh --cortex --glmdir lh.CB10.20.thickness.glmdir
Thank you in advance for your time and effort!
Kind regards, A. Dijkshoorn
please send the fsgd file. Also, send the full text output from mri_glmfit
On 4/3/18 5:49 AM, Dijkshoorn, A.B.C. (Aicha) wrote:
Dear free surfer developers,
When I try to run the mri_glmfit free surfer does not seem to recognise my FSGD file. I believe it has something to do with the underlying languages, since it appears to occur both when I create a plain txt file or when I adjust the tutorials gender_age.fsgd and adjust the values of the covariates. I have tried tons of things to fix the problem, but i can't seem to figure it out... Do you by any chance have an idea on how I can fix this?
error (in bash): ERROR: matrix is ill-conditioned or badly scaled, condno = 15250.9 command line: mri_glmfit --y lh.CB10.thickness.20.mgh --fsgd doesnotworkretestCB10.fsgd doss --C con-hem.mtx --surf fsaverage lh --cortex --glmdir lh.CB10.20.thickness.glmdir Thank you in advance for your time and effort!
Kind regards, A. Dijkshoorn
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The problem is that you only have one subject for group haemorrhage. If you are going to include a covariate, then you need more than one subject
On 04/03/2018 05:49 AM, Dijkshoorn, A.B.C. (Aicha) wrote:
Dear free surfer developers,
When I try to run the mri_glmfit free surfer does not seem to recognise my FSGD file. I believe it has something to do with the underlying languages, since it appears to occur both when I create a plain txt file or when I adjust the tutorials gender_age.fsgd and adjust the values of the covariates. I have tried tons of things to fix the problem, but i can't seem to figure it out... Do you by any chance have an idea on how I can fix this?
error (in bash): ERROR: matrix is ill-conditioned or badly scaled, condno = 15250.9 command line: mri_glmfit --y lh.CB10.thickness.20.mgh --fsgd doesnotworkretestCB10.fsgd doss --C con-hem.mtx --surf fsaverage lh --cortex --glmdir lh.CB10.20.thickness.glmdir Thank you in advance for your time and effort!
Kind regards, A. Dijkshoorn
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
you should also demean your covariate
On 04/03/2018 03:13 PM, Douglas N. Greve wrote:
The problem is that you only have one subject for group haemorrhage. If you are going to include a covariate, then you need more than one subject
On 04/03/2018 05:49 AM, Dijkshoorn, A.B.C. (Aicha) wrote:
Dear free surfer developers,
When I try to run the mri_glmfit free surfer does not seem to recognise my FSGD file. I believe it has something to do with the underlying languages, since it appears to occur both when I create a plain txt file or when I adjust the tutorials gender_age.fsgd and adjust the values of the covariates. I have tried tons of things to fix the problem, but i can't seem to figure it out... Do you by any chance have an idea on how I can fix this?
error (in bash): ERROR: matrix is ill-conditioned or badly scaled, condno = 15250.9 command line: mri_glmfit --y lh.CB10.thickness.20.mgh --fsgd doesnotworkretestCB10.fsgd doss --C con-hem.mtx --surf fsaverage lh --cortex --glmdir lh.CB10.20.thickness.glmdir Thank you in advance for your time and effort!
Kind regards, A. Dijkshoorn
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Sorry, one more thing. I think that it should work if you demean your covariate, no need to have multiple subjects from that group
On 04/03/2018 03:16 PM, Douglas N. Greve wrote:
you should also demean your covariate
On 04/03/2018 03:13 PM, Douglas N. Greve wrote:
The problem is that you only have one subject for group haemorrhage. If you are going to include a covariate, then you need more than one subject
On 04/03/2018 05:49 AM, Dijkshoorn, A.B.C. (Aicha) wrote:
Dear free surfer developers,
When I try to run the mri_glmfit free surfer does not seem to recognise my FSGD file. I believe it has something to do with the underlying languages, since it appears to occur both when I create a plain txt file or when I adjust the tutorials gender_age.fsgd and adjust the values of the covariates. I have tried tons of things to fix the problem, but i can't seem to figure it out... Do you by any chance have an idea on how I can fix this?
error (in bash): ERROR: matrix is ill-conditioned or badly scaled, condno = 15250.9 command line: mri_glmfit --y lh.CB10.thickness.20.mgh --fsgd doesnotworkretestCB10.fsgd doss --C con-hem.mtx --surf fsaverage lh --cortex --glmdir lh.CB10.20.thickness.glmdir Thank you in advance for your time and effort!
Kind regards, A. Dijkshoorn
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Doug,
Demeaning the covariate indeed does seem to work. I did not have to multiply subjects for this.
Thank you so much for your help! ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N. Greve [dgreve@mgh.harvard.edu] Sent: Tuesday, April 03, 2018 9:32 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FSGD file error
Sorry, one more thing. I think that it should work if you demean your covariate, no need to have multiple subjects from that group
On 04/03/2018 03:16 PM, Douglas N. Greve wrote:
you should also demean your covariate
On 04/03/2018 03:13 PM, Douglas N. Greve wrote:
The problem is that you only have one subject for group haemorrhage. If you are going to include a covariate, then you need more than one subject
On 04/03/2018 05:49 AM, Dijkshoorn, A.B.C. (Aicha) wrote:
Dear free surfer developers,
When I try to run the mri_glmfit free surfer does not seem to recognise my FSGD file. I believe it has something to do with the underlying languages, since it appears to occur both when I create a plain txt file or when I adjust the tutorials gender_age.fsgd and adjust the values of the covariates. I have tried tons of things to fix the problem, but i can't seem to figure it out... Do you by any chance have an idea on how I can fix this?
error (in bash): ERROR: matrix is ill-conditioned or badly scaled, condno = 15250.9 command line: mri_glmfit --y lh.CB10.thickness.20.mgh --fsgd doesnotworkretestCB10.fsgd doss --C con-hem.mtx --surf fsaverage lh --cortex --glmdir lh.CB10.20.thickness.glmdir Thank you in advance for your time and effort!
Kind regards, A. Dijkshoorn
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Dijkshoorn, A.B.C. (Aicha) -
Douglas Greve -
Douglas N. Greve