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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February 26, 2004 10:56AM

Given that you have 200 brains to work with... you might consider a semi-automated procedure as briefly outlined below:

1. Obtain the MNI template or other template for the CC. (or u could create your own by creating a probabilistic map of the CC for your 200 brains in talairach space).
2. Align this CC mask into talairach space.
3. Dilate this talairached mask to make it a bit more inclusive.
4. For each subject, transform this talairached mask into the subject's original space.
5. Apply mask onto anatomical data and count voxels that lie within mask and exceed some intensity threshold (which you could determine from finding the white matter peak in the histogram of the anatomical data, be sure to run 3dUniformize before creating the histogram).
6. Compute volume based on the voxel count.

As I type this I realize that this might take as long to implement and test as manually drawing the ROIs, but on the other hand it would be a 'tad' less painful. :)


good luck,
-shruti

Subject Author Posted

calculating volume

jodene February 25, 2004 07:09PM

Re: calculating volume

Ziad S. Saad February 26, 2004 09:39AM

Re: calculating volume

jodene February 26, 2004 10:30AM

Re: calculating volume

Shruti February 26, 2004 10:56AM

Re: calculating volume

jodene February 26, 2004 11:29AM

Re: calculating volume

bob cox February 26, 2004 04:02PM

Re: calculating volume

jodene February 26, 2004 05:19PM

Re: calculating volume

rick reynolds February 27, 2004 08:12AM