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

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Ziad S. Saad
May 04, 2005 03:50PM
Hello all,

You can read BrainVoyager .vmr files and surfaces into AFNI and SUMA.


To change a vmr (say rs_acpc_tal.vmr) file to an AFNI dataset use:
3dBRAIN_VOYAGERtoAFNI -input rs_acpc_tal.vmr
That produces and AFNI dataset: rs_acpc_tal+tlrc.HEAD and rs_acpc_tal+tlrc.BRIK
Launch AFNI with : afni -niml &

To load a BrainVoyager surface (say rs_acpc_tal_LH_WM.srf) into SUMA:
suma -i_bv rs_acpc_tal_LH_WM.srf -sv rs_acpc_tal+tlrc. &

To see the surface atop the volume, press 't' in SUMA etc. etc.

Note 1: You can also load BrainVoyager surfaces using the spec file.
You can create a spec file easily using quickspec:
quickspec -spec bvsample.spec -tn bv rs_acpc_tal_LH_GM.srf -tn bv rs_acpc_tal_LH_WM.srf
Then load the surface using:
suma -spec bvsample.spec -sv rs_acpc_tal+tlrc. &
You will probably want to edit the spec file to setup the relationship between the various surfaces, particularly the LocalDomainParent fields. If you do not know what LocalDomainParent is, search for it here:
[afni.nimh.nih.gov]

Note 2: 3dBRAIN_VOYAGERtoAFNI only reads .vmr files at the moment.
If you REALLY need to read other BrainVoyager volumes, let me know.

New code will be available tonight.
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Reading BrainVoyager .vmr volumes and .srf surfaces

Ziad S. Saad May 04, 2005 03:50PM