Hi Reza, if you look in preproc-sess you will see each of the commands that gets run. You can adapt the command lines from that doug

On 08/24/2014 07:52 PM, Reza Rajimehr wrote:

Hi,

I want to use FreeSurfer v5.3 and its FS-FAST for the functional analysis of monkey data. To have a better control on the parameters of the analysis, I prefer to run the individual commands of preproc-sess one-by-one and check the output of each stage before proceeding with the rest of preproc-sess. Specifically I may manually edit the functional-anatomical registration, so I want to check the registration before moving on to the next step in preproc-sess. Also I need to skip the human-specific aspects of the analysis (e.g. Talairaching) if there are such things in preproc-sess. So is there a list of individual commends, in an appropriate order, that are used in preproc-sess?

If someone has a routine for monkey data analysis with FreeSurfer v5.3, I would be happy to know about that as well.

Thanks, Reza _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer