Hi Rick,

1. Can you run FreeSurfer programs successfully?
Yes, FreeSurfer program runs without any issue.

2. Does "3dAllineate -help" work?
Do you mean running 3dAllineate -help on the terminal? If so, yes it works.

3. Is it suma that is failing exactly like in your initial post?
Please repost the command and output, juuuuust to be sure.

#!/bin/csh
setenv FREESURFER_HOME /Applications/freesurfer
setenv FSFAST_HOME /Applications/freesurfer/fsfast
setenv FSF_OUTPUT_FORMAT nii
setenv SUBJECTS_DIR /PATH
setenv MNI_DIR /Applications/freesurfer/mni
setenv PATH ${FREESURFER_HOME}/bin:${PATH}

@ linenum = 1
set subjlist = (SUBJECT#)
set condlist = (Condition)

foreach subj ($subjlist)
foreach cond ($condlist)

cd /PATH
@SUMA_Make_Spec_FS -sid "$subj"."$cond"

end
end

Other analysis trials worked fine with the same script.

4. If you first start tcsh (just run that command), can you then run suma?

Both bash and tcsh showed the same error.

Thanks,
JW