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

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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