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
|
Ziad
September 18, 2003 12:07PM
Hi Mark,

It looks like you have all the steps you need but I suggest a reshuffling of the steps.

1- 3dVolreg to align all volumes
2- 3dmerge to average them
From this point on you just use the averaged scan
3- 3dUniformize to remove instensity non-uniformity
4- 3dIntracranial to remove skull
5- 3dResample to write out data set in LPI and 1x1x1mm3
(see NOTE under section 'Creating the spec files for SureFit:' on SUMA's documentation page: [afni.nimh.nih.gov])
6- 3dAFNItoMINC and load it to SureFit

This sequence will reduce the number of operations needed and preserves the data in its original format for volume registration and averaging.

cheers,
-z
Reply Quote
RSS
Subject Author Posted

preparing a surface volume

Mark September 17, 2003 11:15PM

Re: preparing a surface volume

Ziad September 18, 2003 12:07PM

Re: preparing a surface volume

Mark September 18, 2003 12:34PM

Re: preparing a surface volume

Ziad September 18, 2003 12:57PM

Re: preparing a surface volume

bob cox September 18, 2003 12:52PM

Re: preparing a surface volume

Mark September 18, 2003 01:05PM