Hi Rachel, I have deleted your previous msg and my response, so I don't know exactly what this is referring to. From the info below, it looks like you need a backslash ("\") after lh.oribitalfrontal.label. Note that you should not specify both --cortex and --label
doug

On 7/31/13 7:20 PM, Rachel Jonas wrote:

Hi Doug,

Thanks for the response. Here is my glmfit command:

mri_glmfit \

--y lh.22q_age.thickness.10.mgh \

--fsgd 22q_age.fsgd dods\

--C 22q_age_2.mtx \

--surf fsaverage lh \

--label lh.orbitofrontal.label

--cortex \

--glmdir lh.22q_age_OFC.glmdir

And here is the error message:

gdfReadHeader: reading 22q_age.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.

Continuous Variable Means (all subjects)

0 age 12.7292

Class Means of each Continuous Variable

1 HC 12.8261

2 22Q 12.6400

INFO: gd2mtx_method is dods

Reading source surface /u/home/FMRI/cbearden/data/22q/Analyses/sMRI/fsaverage/surf/lh.white

ERROR: must specify GLM output dir

[racheljo@login3 sMRI]$ --cortex \

? --glmdir lh.22q_age_OFC.glmdir

--cortex: Command not found.

Thanks!

Rachel
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