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  

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Colm Connolly
May 09, 2006 04:08AM
Hi all,

Based on what Ziad said in his message I gave this a try yesterday evening.

I used the defaults from fsl which yielded these commands lines for the normalisation for the anatomical and functional respectively

/usr/share/fsl/bin/flirt -in /home/colmconn/mriAnalyses/mrUserGroupDemo/data/ts/ctrl/s1/s1.anat.nii -ref /usr/share/fsl/etc/standard/avg152T1_brain.hdr -out /home/colmconn/mriAnalyses/mrUserGroupDemo/data/ts/ctrl/s1/s1.anat.registered.nii -omat /home/colmconn/mriAnalyses/mrUserGroupDemo/data/ts/ctrl/s1/s1.anat.registered.mat -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12 -interp trilinear

/usr/share/fsl/bin/flirt -in /home/colmconn/mriAnalyses/mrUserGroupDemo/data/ts/ctrl/s1/s1.allruns.ed.nii -ref /usr/share/fsl/etc/standard/avg152T1_brain.hdr -out /home/colmconn/mriAnalyses/mrUserGroupDemo/data/ts/ctrl/s1/s1.allruns.ed.registered.nii -omat /home/colmconn/mriAnalyses/mrUserGroupDemo/data/ts/ctrl/s1/s1.allruns.ed.registered.mat -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12 -interp trilinear

You can see the difference in the before and after normalisation screen shots which I've attached.

I haven't tried mcflirt yet. I might give it a go later today.

Bye,

Colm.
Subject Author Posted

How can I aling the functional dataset to the anatomical dataset?

Jiangang Liu April 10, 2006 03:00AM

Re: How can I aling the functional dataset to the anatomical dataset?

Vince April 10, 2006 10:34AM

Re: How can I aling the functional dataset to the anatomical dataset?

Dmitry May 02, 2006 01:05PM

Re: How can I aling the functional dataset to the anatomical dataset?

Ziad Saad May 02, 2006 09:31PM

Re: How can I aling the functional dataset to the anatomical dataset?

Balazs Szemes May 04, 2006 12:47AM

Re: How can I aling the functional dataset to the anatomical dataset?

Colm Connolly May 08, 2006 07:23AM

Re: How can I aling the functional dataset to the anatomical dataset?

Colm Connolly May 09, 2006 04:08AM

Re: How can I aling the functional dataset to the anatomical dataset?

Balazs May 10, 2006 12:10AM

Re: How can I aling the functional dataset to the anatomical dataset?

Colm Connolly May 10, 2006 05:49AM

Re: How can I aling the functional dataset to the anatomical dataset?

Balazs May 10, 2006 01:52PM