AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

Previous Message Next Message
Message List New Topic Print View
|
Godot
November 29, 2005 02:25PM
Hi Ricky,

The -no_ss option is not all that optional.
Here is a table of when you should and should not use -no_ss

Temp. WITH skull Temp. WITHOUT skull
Dset.
WITH skull -no_ss xxx

WITHOUT skull No Cigar -no_ss

Temp. means: Your template of choice
Dset. means: Your anatomical dataset
-no_ss means: Skull stripping should not be attempted on Dset
xxx means: Don't put anything, the script will strip Dset
No Cigar mean: Don't try that combination, it makes no sense.

You do not need to stick with the skull stripped TLRC-ed output. Once you know what the transform is, you can apply it to any other dataset (including the skulled anatomical) with @auto_tlrc in usage mode 2.

cheers,
-G
Reply Quote
RSS
Subject Author Posted

problem using @auto_tlrc using -no_ss flag

Ricky Tong November 29, 2005 01:36PM

Re: problem using @auto_tlrc using -no_ss flag

Godot November 29, 2005 02:25PM

Re: problem using @auto_tlrc using -no_ss flag

Ricky Tong November 29, 2005 05:12PM