you can also use the little-known -avgcurvtifpath and -avgcurvtif flags to specify your own tiff. But you need to make sure to spec them each time you run it.

doug

Bruce Fischl wrote:

Hi Danny,

you're probably better off just editing the recon-all script to change the names of these files.

cheers, Bruce On Mon, 31 May 2010, Danny Kim wrote:

...

Hi all,

I was wondering if there are flags you can specify to use your own .tif and .gcs files in -autorecon3 processing pipeline.

Currently, I am calling up individual processes to double check the results, but in the long run it would be useful to just automate this.

Thanks

Danny,

---

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