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
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:
- 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
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 <greve@nmr.mgh.harvard.edu
wrote:
If you seek help with this problem, make sure to send:
- 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:
- 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 greve@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.
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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> 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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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 <mailto: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
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 <greve@nmr.mgh.harvard.edu
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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> 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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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 <mailto: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 greve@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
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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> 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 > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> 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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://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 <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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 <mailto: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 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 <greve@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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> 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 > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> 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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://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 <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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 <mailto: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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
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 hanbyul.h.cho@gmail.com 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 < greve@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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> 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 > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> 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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://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 <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 sentto
> 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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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 <mailto: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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
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 <greve@nmr.mgh.harvard.edu mailto:greve@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 > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> 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 > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> 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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > Phone Number:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://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 <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 greve@nmr.mgh.harvard.edu 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 <greve@nmr.mgh.harvard.edu mailto:greve@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 > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> 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 othercomputer,
> 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 > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> 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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 tel:617-724-2358>
> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://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 <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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 <mailto:Freesurfer@nmr.mgh.harvard.edu>
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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/
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Douglas N Greve -
Hanbyul Cho