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?highlight=%28mri%5C_glmfit%5C-sim%29

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

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>*
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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