Re: [Freesurfer] Group Analysis: Two Groups and Two Covariates.

2016-06-01 Thread Hanbyul Cho 
Dear Douglas N Greve, FreeSurfer Team,

Thank you for your clear explanation.

Best Wishes,

Han

On Wed, Jun 1, 2016 at 3:55 PM, Douglas N Greve 
wrote:

> Column 5 is completely redundant with column 1 (and highly colinear with
> column 3). Column 6 is nearly identical to column 2 (and highly colinear
> with column 4). This is causing your matrix to be ill-conditioned
>
> On 05/26/2016 02:12 PM, Hanbyul Cho wrote:
> > Dear Douglas N Greve,
> >
> >
> > I sent again this design matrix (= Xg.dat) by attached.
> >
> > Thank you.
> >
> > Han.
> >
> > On Thu, May 26, 2016 at 11:59 AM, Douglas N Greve
> > > wrote:
> >
> > Design matrix, not contrast matrix. It was printed out as part of the
> > terminal output. It can also be found in glmdir/Xg.dat
> >
> > On 05/26/2016 01:48 PM, Hanbyul Cho wrote:
> > > Dear Douglas N Greve,
> > >
> > > The Contrast matrix was = [1 -1 0 0 0 0]
> > > I attached the Xg.dat printed by unended mri_glmfit process.
> > >
> > > Thank you.
> > >
> > > Han.
> > >
> > > On Thu, May 26, 2016 at 10:37 AM, Douglas N Greve
> > > 
> >  > >> wrote:
> > >
> > > Please send the design matrix
> > >
> > > On 05/24/2016 08:05 PM, Hanbyul Cho wrote:
> > > > Dear Douglas N Greve,
> > > >
> > > > Today, I tested the previous group analysis on other
> computer,
> > > and saw
> > > > the same error massage.
> > > >
> > > > I attached the tested fsgd and mtx files.
> > > >
> > > > command:
> > > > mri_glmfit --y 052416_lh.Pa_Co_G2V2_dods_sm15.mgh --fsgd
> > > > 052416_PA_CO_G2V2.fsgd dods --glmdir
> > > > 052416_lh.Pa_Co_G2V2_dods_sm15.glmdir --cortex --surf
> > fsaverage
> > > lh --C
> > > > 052416_contrast.mtx
> > > >
> > > > Thank you,
> > > >
> > > > Best wishes,
> > > >
> > > > Han
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > On Mon, May 23, 2016 at 12:56 PM, Douglas N Greve
> > > >  > 
> >  >>
> > >  > 
> > >  >  > > >
> > > > If you seek help with this problem, make sure to send:
> > > >1. Your command line:
> > > >  mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd
> **.fsgd
> > > dods --C
> > > > **G2V2.mtx --surf fsaverage lh --cortex --glmdir
> > > > lh.**G2V2.dods_sm15.glmdir
> > > >2. The FSGD file (if using one)
> > > >3. And the design matrix above
> > > >
> > > > On 05/21/2016 04:57 PM, Hanbyul Cho wrote:
> > > > > Dear FreeSurfer Team,
> > > > >
> > > > > I processed the Group analysis by FreeSurfer 5.3.0
> > > > >
> > > > > Our data has two groups (Patient, Control) and two
> > > covariate values
> > > > > (age, extra value)
> > > > > mtx, contrast is 1 -1 0 0 0 0
> > > > > The mris_preproc, and mri_surf2surf command were
> > completed
> > > > without error.
> > > > >
> > > > > mris_preproc --fsgd **G2V2.fsgd --target fsaverage
> > --hemi
> > > lh --meas
> > > > > thickness --out lh.**G2V2.dods.mgh
> > > > > mri_surf2surf --hemi lh --s fsaverage --sval
> > > lh.**G2V2.dods.mgh
> > > > --fwhm
> > > > > 15 --cortex --tval lh.**G2V2.dods_sm15.mgh
> > > > > mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd
> > **.fsgd dods --C
> > > > > **G2V2.mtx --surf fsaverage lh --cortex --glmdir
> > > > > lh.**G2V2.dods_sm15.glmdir
> > > > >
> > > > > After mri_glmfit command, I saw the error message.
> > > > >
> > > > >
> > =
> > > > > ERROR: matrix is ill-conditioned or badly scaled,
> > condno =
> > > 1e+08
> > > > > 
> > > > > Possible problem with experimental design:
> > > > > Check for duplicate entries and/or lack of range of
> > > > > continuous variables within a class.
> > > > > If you seek help with this problem, make sure to send:
> > > > >   1. Your

Re: [Freesurfer] Group Analysis: Two Groups and Two Covariates.

2016-06-01 Thread Douglas N Greve 
Column 5 is completely redundant with column 1 (and highly colinear with 
column 3). Column 6 is nearly identical to column 2 (and highly colinear 
with column 4). This is causing your matrix to be ill-conditioned

On 05/26/2016 02:12 PM, Hanbyul Cho wrote:
> Dear Douglas N Greve,
>
>
> I sent again this design matrix (= Xg.dat) by attached.
>
> Thank you.
>
> Han.
>
> On Thu, May 26, 2016 at 11:59 AM, Douglas N Greve 
> > wrote:
>
> Design matrix, not contrast matrix. It was printed out as part of the
> terminal output. It can also be found in glmdir/Xg.dat
>
> On 05/26/2016 01:48 PM, Hanbyul Cho wrote:
> > Dear Douglas N Greve,
> >
> > The Contrast matrix was = [1 -1 0 0 0 0]
> > I attached the Xg.dat printed by unended mri_glmfit process.
> >
> > Thank you.
> >
> > Han.
> >
> > On Thu, May 26, 2016 at 10:37 AM, Douglas N Greve
> > 
>  >> wrote:
> >
> > Please send the design matrix
> >
> > On 05/24/2016 08:05 PM, Hanbyul Cho wrote:
> > > Dear Douglas N Greve,
> > >
> > > Today, I tested the previous group analysis on other computer,
> > and saw
> > > the same error massage.
> > >
> > > I attached the tested fsgd and mtx files.
> > >
> > > command:
> > > mri_glmfit --y 052416_lh.Pa_Co_G2V2_dods_sm15.mgh --fsgd
> > > 052416_PA_CO_G2V2.fsgd dods --glmdir
> > > 052416_lh.Pa_Co_G2V2_dods_sm15.glmdir --cortex --surf
> fsaverage
> > lh --C
> > > 052416_contrast.mtx
> > >
> > > Thank you,
> > >
> > > Best wishes,
> > >
> > > Han
> > >
> > >
> > >
> > >
> > >
> > > On Mon, May 23, 2016 at 12:56 PM, Douglas N Greve
> > >  
> >
> >  
> >   > >
> > > If you seek help with this problem, make sure to send:
> > >1. Your command line:
> > >  mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd
> > dods --C
> > > **G2V2.mtx --surf fsaverage lh --cortex --glmdir
> > > lh.**G2V2.dods_sm15.glmdir
> > >2. The FSGD file (if using one)
> > >3. And the design matrix above
> > >
> > > On 05/21/2016 04:57 PM, Hanbyul Cho wrote:
> > > > Dear FreeSurfer Team,
> > > >
> > > > I processed the Group analysis by FreeSurfer 5.3.0
> > > >
> > > > Our data has two groups (Patient, Control) and two
> > covariate values
> > > > (age, extra value)
> > > > mtx, contrast is 1 -1 0 0 0 0
> > > > The mris_preproc, and mri_surf2surf command were
> completed
> > > without error.
> > > >
> > > > mris_preproc --fsgd **G2V2.fsgd --target fsaverage
> --hemi
> > lh --meas
> > > > thickness --out lh.**G2V2.dods.mgh
> > > > mri_surf2surf --hemi lh --s fsaverage --sval
> > lh.**G2V2.dods.mgh
> > > --fwhm
> > > > 15 --cortex --tval lh.**G2V2.dods_sm15.mgh
> > > > mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd
> **.fsgd dods --C
> > > > **G2V2.mtx --surf fsaverage lh --cortex --glmdir
> > > > lh.**G2V2.dods_sm15.glmdir
> > > >
> > > > After mri_glmfit command, I saw the error message.
> > > >
> > > >
> =
> > > > ERROR: matrix is ill-conditioned or badly scaled,
> condno =
> > 1e+08
> > > > 
> > > > Possible problem with experimental design:
> > > > Check for duplicate entries and/or lack of range of
> > > > continuous variables within a class.
> > > > If you seek help with this problem, make sure to send:
> > > >   1. Your command line:
> > > > mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd
> **.fsgd
> > dods --C
> > > > **G2V2.mtx --surf fsaverage lh --cortex --glmdir
> > > > lh.**G2V2.dods_sm15.glmdir
> > > >   2. The FSGD file (if using one)
> > > >   3. And the design matrix above
> > > >
> =
> >

Re: [Freesurfer] Group Analysis: Two Groups and Two Covariates.

2016-06-01 Thread Hanbyul Cho 
Dear FreeSurfer Team,

I wonder you could not read an previous attached file.

Thank you,
Han

On Thu, May 26, 2016 at 12:12 PM, Hanbyul Cho 
wrote:

> Dear Douglas N Greve,
>
>
> I sent again this design matrix (= Xg.dat) by attached.
>
> Thank you.
>
> Han.
>
> On Thu, May 26, 2016 at 11:59 AM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> Design matrix, not contrast matrix. It was printed out as part of the
>> terminal output. It can also be found in glmdir/Xg.dat
>>
>> On 05/26/2016 01:48 PM, Hanbyul Cho wrote:
>> > Dear Douglas N Greve,
>> >
>> > The Contrast matrix was = [1 -1 0 0 0 0]
>> > I attached the Xg.dat printed by unended mri_glmfit process.
>> >
>> > Thank you.
>> >
>> > Han.
>> >
>> > On Thu, May 26, 2016 at 10:37 AM, Douglas N Greve
>> > > wrote:
>> >
>> > Please send the design matrix
>> >
>> > On 05/24/2016 08:05 PM, Hanbyul Cho wrote:
>> > > Dear Douglas N Greve,
>> > >
>> > > Today, I tested the previous group analysis on other computer,
>> > and saw
>> > > the same error massage.
>> > >
>> > > I attached the tested fsgd and mtx files.
>> > >
>> > > command:
>> > > mri_glmfit --y 052416_lh.Pa_Co_G2V2_dods_sm15.mgh --fsgd
>> > > 052416_PA_CO_G2V2.fsgd dods --glmdir
>> > > 052416_lh.Pa_Co_G2V2_dods_sm15.glmdir --cortex --surf fsaverage
>> > lh --C
>> > > 052416_contrast.mtx
>> > >
>> > > Thank you,
>> > >
>> > > Best wishes,
>> > >
>> > > Han
>> > >
>> > >
>> > >
>> > >
>> > >
>> > > On Mon, May 23, 2016 at 12:56 PM, Douglas N Greve
>> > > 
>> > > > >> wrote:
>> > >
>> > > If you seek help with this problem, make sure to send:
>> > >1. Your command line:
>> > >  mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd
>> > dods --C
>> > > **G2V2.mtx --surf fsaverage lh --cortex --glmdir
>> > > lh.**G2V2.dods_sm15.glmdir
>> > >2. The FSGD file (if using one)
>> > >3. And the design matrix above
>> > >
>> > > On 05/21/2016 04:57 PM, Hanbyul Cho wrote:
>> > > > Dear FreeSurfer Team,
>> > > >
>> > > > I processed the Group analysis by FreeSurfer 5.3.0
>> > > >
>> > > > Our data has two groups (Patient, Control) and two
>> > covariate values
>> > > > (age, extra value)
>> > > > mtx, contrast is 1 -1 0 0 0 0
>> > > > The mris_preproc, and mri_surf2surf command were completed
>> > > without error.
>> > > >
>> > > > mris_preproc --fsgd **G2V2.fsgd --target fsaverage --hemi
>> > lh --meas
>> > > > thickness --out lh.**G2V2.dods.mgh
>> > > > mri_surf2surf --hemi lh --s fsaverage --sval
>> > lh.**G2V2.dods.mgh
>> > > --fwhm
>> > > > 15 --cortex --tval lh.**G2V2.dods_sm15.mgh
>> > > > mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd dods
>> --C
>> > > > **G2V2.mtx --surf fsaverage lh --cortex --glmdir
>> > > > lh.**G2V2.dods_sm15.glmdir
>> > > >
>> > > > After mri_glmfit command, I saw the error message.
>> > > >
>> > > > =
>> > > > ERROR: matrix is ill-conditioned or badly scaled, condno =
>> > 1e+08
>> > > > 
>> > > > Possible problem with experimental design:
>> > > > Check for duplicate entries and/or lack of range of
>> > > > continuous variables within a class.
>> > > > If you seek help with this problem, make sure to send:
>> > > >   1. Your command line:
>> > > > mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd
>> > dods --C
>> > > > **G2V2.mtx --surf fsaverage lh --cortex --glmdir
>> > > > lh.**G2V2.dods_sm15.glmdir
>> > > >   2. The FSGD file (if using one)
>> > > >   3. And the design matrix above
>> > > > =
>> > > >
>> > > > I think our fsgd and mtx compositions are equal to the
>> > g2v2.fsgd
>> > > which
>> > > > FreeSurfer wiki example.
>> > > > (https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V)
>> > > >
>> > > > In this situation, how can I correct my fsgd or mtx files?
>> > Is there
>> > > > any other command option?
>> > > >
>> > > > Best Regards,
>> > > >
>> > > > Han
>> > > >
>> > > >
>> > > > ___
>> > > > Freesurfer mailing list
>> > > > Freesurfer@nmr.mgh.harvard.edu
>> >

Re: [Freesurfer] Group Analysis: Two Groups and Two Covariates.

2016-05-26 Thread Hanbyul Cho 
Dear Douglas N Greve,


I sent again this design matrix (= Xg.dat) by attached.

Thank you.

Han.

On Thu, May 26, 2016 at 11:59 AM, Douglas N Greve  wrote:

> Design matrix, not contrast matrix. It was printed out as part of the
> terminal output. It can also be found in glmdir/Xg.dat
>
> On 05/26/2016 01:48 PM, Hanbyul Cho wrote:
> > Dear Douglas N Greve,
> >
> > The Contrast matrix was = [1 -1 0 0 0 0]
> > I attached the Xg.dat printed by unended mri_glmfit process.
> >
> > Thank you.
> >
> > Han.
> >
> > On Thu, May 26, 2016 at 10:37 AM, Douglas N Greve
> > > wrote:
> >
> > Please send the design matrix
> >
> > On 05/24/2016 08:05 PM, Hanbyul Cho wrote:
> > > Dear Douglas N Greve,
> > >
> > > Today, I tested the previous group analysis on other computer,
> > and saw
> > > the same error massage.
> > >
> > > I attached the tested fsgd and mtx files.
> > >
> > > command:
> > > mri_glmfit --y 052416_lh.Pa_Co_G2V2_dods_sm15.mgh --fsgd
> > > 052416_PA_CO_G2V2.fsgd dods --glmdir
> > > 052416_lh.Pa_Co_G2V2_dods_sm15.glmdir --cortex --surf fsaverage
> > lh --C
> > > 052416_contrast.mtx
> > >
> > > Thank you,
> > >
> > > Best wishes,
> > >
> > > Han
> > >
> > >
> > >
> > >
> > >
> > > On Mon, May 23, 2016 at 12:56 PM, Douglas N Greve
> > > 
> >  > >> wrote:
> > >
> > > If you seek help with this problem, make sure to send:
> > >1. Your command line:
> > >  mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd
> > dods --C
> > > **G2V2.mtx --surf fsaverage lh --cortex --glmdir
> > > lh.**G2V2.dods_sm15.glmdir
> > >2. The FSGD file (if using one)
> > >3. And the design matrix above
> > >
> > > On 05/21/2016 04:57 PM, Hanbyul Cho wrote:
> > > > Dear FreeSurfer Team,
> > > >
> > > > I processed the Group analysis by FreeSurfer 5.3.0
> > > >
> > > > Our data has two groups (Patient, Control) and two
> > covariate values
> > > > (age, extra value)
> > > > mtx, contrast is 1 -1 0 0 0 0
> > > > The mris_preproc, and mri_surf2surf command were completed
> > > without error.
> > > >
> > > > mris_preproc --fsgd **G2V2.fsgd --target fsaverage --hemi
> > lh --meas
> > > > thickness --out lh.**G2V2.dods.mgh
> > > > mri_surf2surf --hemi lh --s fsaverage --sval
> > lh.**G2V2.dods.mgh
> > > --fwhm
> > > > 15 --cortex --tval lh.**G2V2.dods_sm15.mgh
> > > > mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd dods
> --C
> > > > **G2V2.mtx --surf fsaverage lh --cortex --glmdir
> > > > lh.**G2V2.dods_sm15.glmdir
> > > >
> > > > After mri_glmfit command, I saw the error message.
> > > >
> > > > =
> > > > ERROR: matrix is ill-conditioned or badly scaled, condno =
> > 1e+08
> > > > 
> > > > Possible problem with experimental design:
> > > > Check for duplicate entries and/or lack of range of
> > > > continuous variables within a class.
> > > > If you seek help with this problem, make sure to send:
> > > >   1. Your command line:
> > > > mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd
> > dods --C
> > > > **G2V2.mtx --surf fsaverage lh --cortex --glmdir
> > > > lh.**G2V2.dods_sm15.glmdir
> > > >   2. The FSGD file (if using one)
> > > >   3. And the design matrix above
> > > > =
> > > >
> > > > I think our fsgd and mtx compositions are equal to the
> > g2v2.fsgd
> > > which
> > > > FreeSurfer wiki example.
> > > > (https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V)
> > > >
> > > > In this situation, how can I correct my fsgd or mtx files?
> > Is there
> > > > any other command option?
> > > >
> > > > Best Regards,
> > > >
> > > > Han
> > > >
> > > >
> > > > ___
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > >  > >
> > > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > > --
> > > Douglas N. Greve, Ph.D.
> > > MGH-NMR Center
> > >

Re: [Freesurfer] Group Analysis: Two Groups and Two Covariates.

2016-05-26 Thread Douglas N Greve 
Design matrix, not contrast matrix. It was printed out as part of the 
terminal output. It can also be found in glmdir/Xg.dat

On 05/26/2016 01:48 PM, Hanbyul Cho wrote:
> Dear Douglas N Greve,
>
> The Contrast matrix was = [1 -1 0 0 0 0]
> I attached the Xg.dat printed by unended mri_glmfit process.
>
> Thank you.
>
> Han.
>
> On Thu, May 26, 2016 at 10:37 AM, Douglas N Greve 
> > wrote:
>
> Please send the design matrix
>
> On 05/24/2016 08:05 PM, Hanbyul Cho wrote:
> > Dear Douglas N Greve,
> >
> > Today, I tested the previous group analysis on other computer,
> and saw
> > the same error massage.
> >
> > I attached the tested fsgd and mtx files.
> >
> > command:
> > mri_glmfit --y 052416_lh.Pa_Co_G2V2_dods_sm15.mgh --fsgd
> > 052416_PA_CO_G2V2.fsgd dods --glmdir
> > 052416_lh.Pa_Co_G2V2_dods_sm15.glmdir --cortex --surf fsaverage
> lh --C
> > 052416_contrast.mtx
> >
> > Thank you,
> >
> > Best wishes,
> >
> > Han
> >
> >
> >
> >
> >
> > On Mon, May 23, 2016 at 12:56 PM, Douglas N Greve
> > 
>  >> wrote:
> >
> > If you seek help with this problem, make sure to send:
> >1. Your command line:
> >  mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd
> dods --C
> > **G2V2.mtx --surf fsaverage lh --cortex --glmdir
> > lh.**G2V2.dods_sm15.glmdir
> >2. The FSGD file (if using one)
> >3. And the design matrix above
> >
> > On 05/21/2016 04:57 PM, Hanbyul Cho wrote:
> > > Dear FreeSurfer Team,
> > >
> > > I processed the Group analysis by FreeSurfer 5.3.0
> > >
> > > Our data has two groups (Patient, Control) and two
> covariate values
> > > (age, extra value)
> > > mtx, contrast is 1 -1 0 0 0 0
> > > The mris_preproc, and mri_surf2surf command were completed
> > without error.
> > >
> > > mris_preproc --fsgd **G2V2.fsgd --target fsaverage --hemi
> lh --meas
> > > thickness --out lh.**G2V2.dods.mgh
> > > mri_surf2surf --hemi lh --s fsaverage --sval
> lh.**G2V2.dods.mgh
> > --fwhm
> > > 15 --cortex --tval lh.**G2V2.dods_sm15.mgh
> > > mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd dods --C
> > > **G2V2.mtx --surf fsaverage lh --cortex --glmdir
> > > lh.**G2V2.dods_sm15.glmdir
> > >
> > > After mri_glmfit command, I saw the error message.
> > >
> > > =
> > > ERROR: matrix is ill-conditioned or badly scaled, condno =
> 1e+08
> > > 
> > > Possible problem with experimental design:
> > > Check for duplicate entries and/or lack of range of
> > > continuous variables within a class.
> > > If you seek help with this problem, make sure to send:
> > >   1. Your command line:
> > > mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd
> dods --C
> > > **G2V2.mtx --surf fsaverage lh --cortex --glmdir
> > > lh.**G2V2.dods_sm15.glmdir
> > >   2. The FSGD file (if using one)
> > >   3. And the design matrix above
> > > =
> > >
> > > I think our fsgd and mtx compositions are equal to the
> g2v2.fsgd
> > which
> > > FreeSurfer wiki example.
> > > (https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V)
> > >
> > > In this situation, how can I correct my fsgd or mtx files?
> Is there
> > > any other command option?
> > >
> > > Best Regards,
> > >
> > > Han
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> 
> >  >
> > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu 
> >
> > Phone Number: 617-724-2358 
> >
> > Fax: 617-726-7422   >
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> > 
> > FileDrop:

Re: [Freesurfer] Group Analysis: Two Groups and Two Covariates.

2016-05-26 Thread Hanbyul Cho 
Dear Douglas N Greve,

The Contrast matrix was = [1 -1 0 0 0 0]
I attached the Xg.dat printed by unended mri_glmfit process.

Thank you.

Han.

On Thu, May 26, 2016 at 10:37 AM, Douglas N Greve  wrote:

> Please send the design matrix
>
> On 05/24/2016 08:05 PM, Hanbyul Cho wrote:
> > Dear Douglas N Greve,
> >
> > Today, I tested the previous group analysis on other computer, and saw
> > the same error massage.
> >
> > I attached the tested fsgd and mtx files.
> >
> > command:
> > mri_glmfit --y 052416_lh.Pa_Co_G2V2_dods_sm15.mgh --fsgd
> > 052416_PA_CO_G2V2.fsgd dods --glmdir
> > 052416_lh.Pa_Co_G2V2_dods_sm15.glmdir --cortex --surf fsaverage lh --C
> > 052416_contrast.mtx
> >
> > Thank you,
> >
> > Best wishes,
> >
> > Han
> >
> >
> >
> >
> >
> > On Mon, May 23, 2016 at 12:56 PM, Douglas N Greve
> > > wrote:
> >
> > If you seek help with this problem, make sure to send:
> >1. Your command line:
> >  mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd dods --C
> > **G2V2.mtx --surf fsaverage lh --cortex --glmdir
> > lh.**G2V2.dods_sm15.glmdir
> >2. The FSGD file (if using one)
> >3. And the design matrix above
> >
> > On 05/21/2016 04:57 PM, Hanbyul Cho wrote:
> > > Dear FreeSurfer Team,
> > >
> > > I processed the Group analysis by FreeSurfer 5.3.0
> > >
> > > Our data has two groups (Patient, Control) and two covariate values
> > > (age, extra value)
> > > mtx, contrast is 1 -1 0 0 0 0
> > > The mris_preproc, and mri_surf2surf command were completed
> > without error.
> > >
> > > mris_preproc --fsgd **G2V2.fsgd --target fsaverage --hemi lh --meas
> > > thickness --out lh.**G2V2.dods.mgh
> > > mri_surf2surf --hemi lh --s fsaverage --sval lh.**G2V2.dods.mgh
> > --fwhm
> > > 15 --cortex --tval lh.**G2V2.dods_sm15.mgh
> > > mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd dods --C
> > > **G2V2.mtx --surf fsaverage lh --cortex --glmdir
> > > lh.**G2V2.dods_sm15.glmdir
> > >
> > > After mri_glmfit command, I saw the error message.
> > >
> > > =
> > > ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
> > > 
> > > Possible problem with experimental design:
> > > Check for duplicate entries and/or lack of range of
> > > continuous variables within a class.
> > > If you seek help with this problem, make sure to send:
> > >   1. Your command line:
> > > mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd dods --C
> > > **G2V2.mtx --surf fsaverage lh --cortex --glmdir
> > > lh.**G2V2.dods_sm15.glmdir
> > >   2. The FSGD file (if using one)
> > >   3. And the design matrix above
> > > =
> > >
> > > I think our fsgd and mtx compositions are equal to the g2v2.fsgd
> > which
> > > FreeSurfer wiki example.
> > > (https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V)
> > >
> > > In this situation, how can I correct my fsgd or mtx files? Is there
> > > any other command option?
> > >
> > > Best Regards,
> > >
> > > Han
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu 
> > Phone Number: 617-724-2358 
> > Fax: 617-726-7422 
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > 
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > 
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu  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 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.
> >
> >
> >
>

Re: [Freesurfer] Group Analysis: Two Groups and Two Covariates.

2016-05-26 Thread Douglas N Greve 
Please send the design matrix

On 05/24/2016 08:05 PM, Hanbyul Cho wrote:
> Dear Douglas N Greve,
>
> Today, I tested the previous group analysis on other computer, and saw 
> the same error massage.
>
> I attached the tested fsgd and mtx files.
>
> command:
> mri_glmfit --y 052416_lh.Pa_Co_G2V2_dods_sm15.mgh --fsgd 
> 052416_PA_CO_G2V2.fsgd dods --glmdir 
> 052416_lh.Pa_Co_G2V2_dods_sm15.glmdir --cortex --surf fsaverage lh --C 
> 052416_contrast.mtx
>
> Thank you,
>
> Best wishes,
>
> Han
>
>
>
>
>
> On Mon, May 23, 2016 at 12:56 PM, Douglas N Greve 
> > wrote:
>
> If you seek help with this problem, make sure to send:
>1. Your command line:
>  mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd dods --C
> **G2V2.mtx --surf fsaverage lh --cortex --glmdir
> lh.**G2V2.dods_sm15.glmdir
>2. The FSGD file (if using one)
>3. And the design matrix above
>
> On 05/21/2016 04:57 PM, Hanbyul Cho wrote:
> > Dear FreeSurfer Team,
> >
> > I processed the Group analysis by FreeSurfer 5.3.0
> >
> > Our data has two groups (Patient, Control) and two covariate values
> > (age, extra value)
> > mtx, contrast is 1 -1 0 0 0 0
> > The mris_preproc, and mri_surf2surf command were completed
> without error.
> >
> > mris_preproc --fsgd **G2V2.fsgd --target fsaverage --hemi lh --meas
> > thickness --out lh.**G2V2.dods.mgh
> > mri_surf2surf --hemi lh --s fsaverage --sval lh.**G2V2.dods.mgh
> --fwhm
> > 15 --cortex --tval lh.**G2V2.dods_sm15.mgh
> > mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd dods --C
> > **G2V2.mtx --surf fsaverage lh --cortex --glmdir
> > lh.**G2V2.dods_sm15.glmdir
> >
> > After mri_glmfit command, I saw the error message.
> >
> > =
> > ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
> > 
> > Possible problem with experimental design:
> > Check for duplicate entries and/or lack of range of
> > continuous variables within a class.
> > If you seek help with this problem, make sure to send:
> >   1. Your command line:
> > mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd dods --C
> > **G2V2.mtx --surf fsaverage lh --cortex --glmdir
> > lh.**G2V2.dods_sm15.glmdir
> >   2. The FSGD file (if using one)
> >   3. And the design matrix above
> > =
> >
> > I think our fsgd and mtx compositions are equal to the g2v2.fsgd
> which
> > FreeSurfer wiki example.
> > (https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V)
> >
> > In this situation, how can I correct my fsgd or mtx files? Is there
> > any other command option?
> >
> > Best Regards,
> >
> > Han
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> 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 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.
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:

Re: [Freesurfer] Group Analysis: Two Groups and Two Covariates.

2016-05-23 Thread Douglas N Greve 
If you seek help with this problem, make sure to send:
   1. Your command line:
 mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd dods --C 
**G2V2.mtx --surf fsaverage lh --cortex --glmdir lh.**G2V2.dods_sm15.glmdir
   2. The FSGD file (if using one)
   3. And the design matrix above

On 05/21/2016 04:57 PM, Hanbyul Cho wrote:
> Dear FreeSurfer Team,
>
> I processed the Group analysis by FreeSurfer 5.3.0
>
> Our data has two groups (Patient, Control) and two covariate values 
> (age, extra value)
> mtx, contrast is 1 -1 0 0 0 0
> The mris_preproc, and mri_surf2surf command were completed without error.
>
> mris_preproc --fsgd **G2V2.fsgd --target fsaverage --hemi lh --meas 
> thickness --out lh.**G2V2.dods.mgh
> mri_surf2surf --hemi lh --s fsaverage --sval lh.**G2V2.dods.mgh --fwhm 
> 15 --cortex --tval lh.**G2V2.dods_sm15.mgh
> mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd dods --C 
> **G2V2.mtx --surf fsaverage lh --cortex --glmdir 
> lh.**G2V2.dods_sm15.glmdir
>
> After mri_glmfit command, I saw the error message.
>
> =
> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
> 
> Possible problem with experimental design:
> Check for duplicate entries and/or lack of range of
> continuous variables within a class.
> If you seek help with this problem, make sure to send:
>   1. Your command line:
> mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd dods --C 
> **G2V2.mtx --surf fsaverage lh --cortex --glmdir 
> lh.**G2V2.dods_sm15.glmdir
>   2. The FSGD file (if using one)
>   3. And the design matrix above
> =
>
> I think our fsgd and mtx compositions are equal to the g2v2.fsgd which 
> FreeSurfer wiki example.
> (https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V)
>
> In this situation, how can I correct my fsgd or mtx files? Is there 
> any other command option?
>
> Best Regards,
>
> Han
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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 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.

[Freesurfer] Group Analysis: Two Groups and Two Covariates.

2016-05-21 Thread Hanbyul Cho 
Dear FreeSurfer Team,

I processed the Group analysis by FreeSurfer 5.3.0

Our data has two groups (Patient, Control) and two covariate values (age,
extra value)
mtx, contrast is 1 -1 0 0 0 0
The mris_preproc, and mri_surf2surf command were completed without error.

mris_preproc --fsgd **G2V2.fsgd --target fsaverage --hemi lh --meas
thickness --out lh.**G2V2.dods.mgh
mri_surf2surf --hemi lh --s fsaverage --sval lh.**G2V2.dods.mgh --fwhm 15
--cortex --tval lh.**G2V2.dods_sm15.mgh
mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd dods --C **G2V2.mtx
--surf fsaverage lh --cortex --glmdir lh.**G2V2.dods_sm15.glmdir

After mri_glmfit command, I saw the error message.

=
ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
  1. Your command line:
mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd dods --C
**G2V2.mtx --surf fsaverage lh --cortex --glmdir lh.**G2V2.dods_sm15.glmdir
  2. The FSGD file (if using one)
  3. And the design matrix above
=

I think our fsgd and mtx compositions are equal to the g2v2.fsgd which
FreeSurfer wiki example.
(https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V)

In this situation, how can I correct my fsgd or mtx files? Is there any
other command option?

Best Regards,

Han
___
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 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.