Hi Jared,

the names in the two should be the same. That is "your_subject_name" needs to be the same as <subjid> (-s is shorthand for --subjid). If you don't give it input volumes it will assume things are in standardized places.

cheers, Bruce

On Tue, 5 Feb 2008, Jared Morton wrote:

When I run the first portion of the recon-all script according to the instructions in RecommendedReconstruction, the command I am instructed to use is:

*recon-all -i **invol1** -i **invol2** -autorecon1 -subjid ** your_subject_name*

This command allows me to specify the input files and assign them a name.

When I try to run the entire recon-all script according to the instructions in FSTutorial/MorphAndRecon, I am instructed to use this command:

*recon-all -autorecon-all -s <subjid>*

However, unlike the script for the first portion of the recon-all script, there does not appear to be anything in this command that allows me to specify my input files and assign them a name. Because my subject name is not specified, I cannot get the recon-all script to run. How do I assign a subject name without having to run the first portion of the recon-all script? Any help will be greatly appreciated.