Yes, that should work, except you will need to add --perm-resid. See the --help
On 09/13/2017 02:33 PM, Martin Juneja wrote:
Hi experts,
To calculate simulations on LGI measures, I ran: mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --sim perm 1000 3 permcsd --sim-sign abs --cwpvalthresh .05
But it gives error: ERROR: design matrix is not orthogonal, cannot be used with permutation.
I came across a post where its mentioned that: "Alternatively, I have a version of mri_glmfit-sim that will run permutation with non-orthogonal designs. https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_glmfit-sim https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_glmfit-sim"
- Douglas N. Greve
So I was wondering if I can use this program for LGI measures and run the same command, lets say this new program is: mri_glmfit-sim_new, so can I run the following command (instead of doing PALM):
mri_glmfit-sim_new --glmdir lh.MEQ_LGI.glmdir --sim perm 1000 3 permcsd --sim-sign abs --cwpvalthresh .05
Thanks.
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