Hi, don't use --label and --mask. doug
On 10/2/12 9:15 PM, Brain Apprentice wrote: > 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 > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
