Dear FreeSurfer experts,
When I try to run mri_glmfit-sim, the output came out like this:
cmdline mri_glmfit.bin --y lh.gender_age.thickness.10.mgh --fsgd lh.gender-age.fsgd --C lh-Avg-thickness-FemaleMale.age.mtx --C lh-Avg-thickness-FemaleMale.intercept.mtx --C lh-Avg-thickness-Gender.diff.mtx --C lh-Avg-thickness-Gender*Age-Inter.mtx --surf fsaverage lh --cortex --glmdir lh.gender_age.glmdir SURFACE: fsaverage lh set: No match. [toibigi2007@localhost glm1]$ mri_glmfit-sim --help
After I ran the command line like the following: mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 2 neg --cwp 0.05 --2spaces
Please point me out what goes wrong with this command. Any help would be appreciated!
Thank you and warmest regards, *--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme@gmail.com duy.nguyenbme@gmail.com*
Can you add --debug as the first argument and send the terminal output?
On 05/19/2017 11:48 PM, Duy Nguyen wrote:
Dear FreeSurfer experts,
When I try to run mri_glmfit-sim, the output came out like this:
cmdline mri_glmfit.bin --y lh.gender_age.thickness.10.mgh --fsgd lh.gender-age.fsgd --C lh-Avg-thickness-FemaleMale.age.mtx --C lh-Avg-thickness-FemaleMale.intercept.mtx --C lh-Avg-thickness-Gender.diff.mtx --C lh-Avg-thickness-Gender*Age-Inter.mtx --surf fsaverage lh --cortex --glmdir lh.gender_age.glmdir SURFACE: fsaverage lh set: No match. [toibigi2007@localhost glm1]$ mri_glmfit-sim --help
After I ran the command line like the following: mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 2 neg --cwp 0.05 --2spaces
Please point me out what goes wrong with this command. Any help would be appreciated!
Thank you and warmest regards, *--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme@gmail.com mailto:duy.nguyenbme@gmail.com*
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Doug
After I add --debug like this: mri_glmfit-sim --debug --glmdir lh.gender_age.glmdir --cache 3 abs --cwp .999 --2spaces
The terminal output is shown in the attached file.
A bit overview about my analysis: I have 148 subjects that I am interested in analyzing the gender and cortical thickness along with the co-variate age
The fsgd looks like this: GroupDescriptorFile 1 Title lh.gender_age.glmdir MeasurementName LH_CorticalThickness Class Male Class Female Variables Age Input OAS1_0001_MR1 Female 74 Input OAS1_0002_MR1 Female 55 etc ...
I have followed exactly like the step from FreeSurfer Group Analysis website: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0?highl... including in an order: mris_preproc --fsgd lh.gender-age.fsgd --target fsaverage --hemi lh --meas thickness --out lh.gender_age.thickness.00.mgh
mri_surf2surf --hemi lh --s fsaverage --sval lh.gender_age.thickness.00.mgh --fwhm 10 --cortex --tval lh.gender_age.thickness.10.mgh
mri_glmfit --y lh.gender_age.thickness.10.mgh --fsgd lh.gender_age.fsgd --C lh-Avg-thickness-FemaleMale.age.mtx --C lh-Avg-thickness-FemaleMale.intercept.mtx --C lh-Avg-thickness-Gender.diff.mtx --C lh-Avg-thickness-Gender*Age-Inter.mtx --surf fsaverage lh --cortex --yhat-save --glmdir lh.gender_age.glmdir
Please help me figure this out. Anything you would have me to provided, please tell me.
Thank you and warmest regards,
*--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme@gmail.com duy.nguyenbme@gmail.com*
On Mon, May 22, 2017 at 9:57 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Can you add --debug as the first argument and send the terminal output?
On 05/19/2017 11:48 PM, Duy Nguyen wrote:
Dear FreeSurfer experts,
When I try to run mri_glmfit-sim, the output came out like this:
cmdline mri_glmfit.bin --y lh.gender_age.thickness.10.mgh --fsgd lh.gender-age.fsgd --C lh-Avg-thickness-FemaleMale.age.mtx --C lh-Avg-thickness-FemaleMale.intercept.mtx --C lh-Avg-thickness-Gender.diff.mtx --C lh-Avg-thickness-Gender*Age-Inter.mtx --surf fsaverage lh --cortex --glmdir lh.gender_age.glmdir SURFACE: fsaverage lh set: No match. [toibigi2007@localhost glm1]$ mri_glmfit-sim --help
After I ran the command line like the following: mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 2 neg --cwp 0.05 --2spaces
Please point me out what goes wrong with this command. Any help would be appreciated!
Thank you and warmest regards, *--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme@gmail.com mailto:duy.nguyenbme@gmail.com*
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/
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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.
Did you name one of your contrasts "lh-Avg-thickness-Gender*Age-Inter.mtx"? If so, then remove the star ("*") as that has special meaning to the shell
On 5/26/17 2:11 AM, Duy Nguyen wrote:
Dear Doug
After I add --debug like this: mri_glmfit-sim --debug --glmdir lh.gender_age.glmdir --cache 3 abs --cwp .999 --2spaces
The terminal output is shown in the attached file.
A bit overview about my analysis: I have 148 subjects that I am interested in analyzing the gender and cortical thickness along with the co-variate age
The fsgd looks like this: GroupDescriptorFile 1 Title lh.gender_age.glmdir MeasurementName LH_CorticalThickness Class Male Class Female Variables Age Input OAS1_0001_MR1 Female 74 Input OAS1_0002_MR1 Female 55 etc ...
I have followed exactly like the step from FreeSurfer Group Analysis website: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0?highl... including in an order: mris_preproc --fsgd lh.gender-age.fsgd --target fsaverage --hemi lh --meas thickness --out lh.gender_age.thickness.00.mgh
mri_surf2surf --hemi lh --s fsaverage --sval lh.gender_age.thickness.00.mgh --fwhm 10 --cortex --tval lh.gender_age.thickness.10.mgh
mri_glmfit --y lh.gender_age.thickness.10.mgh --fsgd lh.gender_age.fsgd --C lh-Avg-thickness-FemaleMale.age.mtx --C lh-Avg-thickness-FemaleMale.intercept.mtx --C lh-Avg-thickness-Gender.diff.mtx --C lh-Avg-thickness-Gender*Age-Inter.mtx --surf fsaverage lh --cortex --yhat-save --glmdir lh.gender_age.glmdir
Please help me figure this out. Anything you would have me to provided, please tell me.
Thank you and warmest regards,
*--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme@gmail.com mailto:duy.nguyenbme@gmail.com*
On Mon, May 22, 2017 at 9:57 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Can you add --debug as the first argument and send the terminal output? On 05/19/2017 11:48 PM, Duy Nguyen wrote: > Dear FreeSurfer experts, > > When I try to run mri_glmfit-sim, the output came out like this: > > cmdline mri_glmfit.bin --y lh.gender_age.thickness.10.mgh --fsgd > lh.gender-age.fsgd --C lh-Avg-thickness-FemaleMale.age.mtx --C > lh-Avg-thickness-FemaleMale.intercept.mtx --C > lh-Avg-thickness-Gender.diff.mtx --C > lh-Avg-thickness-Gender*Age-Inter.mtx --surf fsaverage lh --cortex > --glmdir lh.gender_age.glmdir > SURFACE: fsaverage lh > set: No match. > [toibigi2007@localhost glm1]$ mri_glmfit-sim --help > > After I ran the command line like the following: > mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 2 neg --cwp 0.05 > --2spaces > > Please point me out what goes wrong with this command. > Any help would be appreciated! > > Thank you and warmest regards, > *--v-- Peace --v--* > *Duy Nguyễn * > *Biomedical Engineering Department- IU HCMC* > *Cell: (+84)909999056* > *Email: duy.nguyenbme@gmail.com <mailto:duy.nguyenbme@gmail.com> <mailto:duy.nguyenbme@gmail.com <mailto:duy.nguyenbme@gmail.com>>* > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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/ <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 <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 <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.
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Douglas N Greve
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Duy Nguyen