Sebastian Moeller wrote:
Dear Doug, dear fsfast experts,
now that the shinny new FreeSurfer has its first point release I got around playing with its FSFAST version (befor I forget freesurfer- Linux-centos4_x86_64-stable-pub-v4.0.1-full, on 64 bit SUSE 10.1). I looks like a lot was changed under the hood (and improved I am sure) now my old scripts certainly need some help to keep going. My first stumbling block is spatialsmooth-sess, which complaines about a missing "ip" binary, (and rightly so, since ip got folded into fslmaths, I fathom). 1. Please let me know, what the recommended replacement for spatialsmooth-sess is nowadays.
I changed from ip to my own program, but this was not done until after the release. However, it should have been in the minor release that Nick released a few weeks after version 4. Are you using that one?
2. And while I am asking, can I truly switch FSFAST defaultformats by "export FSF_OUTPUT_FORMAT=whatever" before sourcing SetUpFreeSurfer?
Yes, it should autodected any format on the input and write out in the format specified by FSF_OUTPUT_FORMAT.
3. I would be happy about a link to a newer tutorial/howto fsf touse as a template to "modernize" my scripts
Here you go: https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial
thank you very much for the powerful tools as always & ahoi Sebastian
doug