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 default
formats 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 to
use 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
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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