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
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