Hello everyone,
I am trying to incorporate a binary FMRI mask into mri_glmfit. The problem is that it does not matter what I put in for the mask file I get the same results.
This is the command I am using:
mri_glmfit \ --y /shared/subjects/4-aut-v510/a-aut-v510/3-long/qdec/test2/y.mgh \ --fsgd /shared/subjects/4-aut-v510/a-aut-v510/3-long/qdec/test2/qdec.fsgd dods \ --glmdir /shared/subjects/4-aut-v510/a-aut-v510/3-long/qdec/test2-msk6 \ --surf fsaverage lh \ --mask /shared/subjects/4-aut-v510/a-aut-v510/3-long/<Files listed below>\ --label /shared/subjects/4-aut-v510/a-aut-v510/3-long/fsaverage/label/lh.aparc.label \ --C /shared/subjects/4-aut-v510/a-aut-v510/3-long/qdec/test2/contrasts/lh-Avg-Intercept-thickness.mat \ --C /shared/subjects/4-aut-v510/a-aut-v510/3-long/qdec/test2/contrasts/lh-Avg-thickness-TOMAL_COMPOSITE_MEMORY_INDEX-Cor.mat \ --C /shared/subjects/4-aut-v510/a-aut-v510/3-long/qdec/test2/contrasts/lh-Diff-Control-ASD-Intercept-thickness.mat \ --C /shared/subjects/4-aut-v510/a-aut-v510/3-long/qdec/test2/contrasts/lh-Diff-Control-ASD-Cor-thickness-TOMAL_COMPOSITE_MEMORY_INDEX.mat
Here are the files that are getting inserted: DMN-b.mgz - Is a binary version of FMRI activation. DMN2-b.mgz - Is a binary file with nothing but zeros. DMN3-b.mgz - Is a binary file with nothing but ones..
I should also point out that the glmdir directory is changing with each new run of mri_glmfit. There is one other thing I should mention, and that is the above command other than the --mask part I got from qdec including the contrast1.mat part.
I am sure it is me and I am doing something wrong. If someone can suggest an alternative I would be most grateful.
Thanks