Hi Dr. Greve,

I tried to run: mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --sim perm 1000 3 permcsd --sim-sign abs --cwpvalthresh .05
It gives error that ERROR: design matrix is not orthogonal, cannot be used with permutation.

But when I run: mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --sim perm 1000 3 permcsd --sim-sign abs --cwpvalthresh .05 --perm-force, it works.

I am not sure whether I will have to make the design matrix orthogonal. If so, could you please tell me how that can be done?

Or using --perm-force should be fine?

Thanks.

On Mon, Mar 6, 2017 at 1:58 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:
This is a problem with using LGI in that it is already extremely smooth
that the smoothness exceeds the limit of the look up table that we
supply. I  recommend that you not use a gaussian-based correction for
LGI. Instead, use permutation (see mri_glmfit-sim --help).



On 03/06/2017 01:36 PM, Martin Juneja wrote:
> Hello everyone,
>
> I am trying to extract clusters showing significant correlation
> between LGI and a behavioral measure. I am able to extract PCC and
> sig.mgh but at the last step when I try to run simulation command to
> view corrected results and I run:
>
> mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --cache 4 neg --cwp 0.05
> --2spaces
>
> I get following error:
>
> ERROR: cannot find
> /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm35/neg/th40/mc-z.csd
>
> But I can see mc-z.csd file in fwhm30 etc.
>
> Full message on terminal window is attached following.
>
> Any help would be really appreciated.
>
> ----- Full message ----
>
> cmdline mri_glmfit.bin --y lh.MEQ_LGI.10.mgh --fsgd MEQ.fsgd dods --C
> Corr-MEQ-cor.mtx --surf fsaverage lh --cortex --glmdir lh.MEQ_LGI.glmdir
>
> WARNING: unrecognized mri_glmfit cmd option mri_glmfit.bin
>
> SURFACE: fsaverage lh
>
> log file is lh.MEQ_LGI.glmdir/cache.mri_glmfit-sim.log
>
> /usr/local/freesurfer/bin/mri_glmfit-sim
>
> --glmdir lh.MEQ_LGI.glmdir --cache 4 neg --cwp 0.05 --2spaces
>
> $Id: mri_glmfit-sim,v 1.60 2016/04/30 15:13:36 greve Exp $
>
> Mon Mar  6 11:11:13 MST 2017
>
> setenv SUBJECTS_DIR
> /data/emot/Freesurfer/FreeSurferSegmentation/SB_AgingAll
>
> FREESURFER_HOME /usr/local/freesurfer
>
> Original mri_glmfit command line:
>
> cmdline mri_glmfit.bin --y lh.MEQ_LGI.10.mgh --fsgd MEQ.fsgd dods --C
> Corr-MEQ-cor.mtx --surf fsaverage lh --cortex --glmdir lh.MEQ_LGI.glmdir
>
> DoSim = 0
>
> UseCache = 1
>
> DoPoll = 0
>
> DoPBSubmit = 0
>
> DoBackground = 0
>
> DiagCluster = 0
>
> gd2mtx = dods
>
> fwhm = 35.073391
>
> ERROR: cannot find
> /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm35/neg/th40/mc-z.csd
>
>
>
> _______________________________________________
> Freesurfer mailing list
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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

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