My guess is that you have a rogue white space after the backslash in "dods ". Try putting the entire command on one line without backslashs

On 3/27/18 6:29 AM, Naiara Aguirre Vidal wrote:

Dear FreeSurfer experts, I have a problem with mri_glmfit.

I am using the following script: mri_glmfit \ --y lh.AspergerStudy.thickness.10.mgh \ --fsgd FSGD/AspergerStudy.fsgd dods \ --C Contrasts/AS-HC.mtx \ --C Contrasts/HC-AS.mtx \ --surf fsaverage lh \ --cortex \ --glmdir lh.thickness.AspergerStudy.10.glmdir But when I run it, I obtain an error: acad1215inv:01_freesurfer_processing acad1215inv$ mri_glmfit \

...

--y lh.AspergerStudy.thickness.10.mgh \ > --fsgd

FSGD/AspergerStudy.fsgd dods \ > --C Contrasts/AS-HC.mtx \ gdfRead(): reading FSGD/AspergerStudy.fsgd INFO: gd2mtx_method is dods ERROR: must specify GLM output dir acad1215inv:01_freesurfer_processing acad1215inv$ --C Contrasts/HC-AS.mtx \ > --surface fsaverage lh \ > --cortex \ > --glmdir lh.thickness.AspergerStudy.10.glmdir -bash: --C: command not found What could I do for solving this problem?

Thanks a lot Naiara

-- *Naiara Aguirre Vidal* Neuropsychology and Functional Neuroimaging group Department of Basic and Clinical Psychology and Psychobiology Jaume I University Edificio de Investigación II, Avda. Sos Baynat, s/n E-12071 Castellón de la Plana (Spain)

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