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
January 06, 2011 10:25AM
Hi Chris,

The problem is now fixed. It was an evil combination of sparse data, cmask, and a compiler optimizer bug! This should all be sorted out now.

AFNI binaries postdating this message will contain the fix.

Note, that your detrending order is a little low. This detrending is meant to remove anatomical structure in the image and reduce activation signal components. You want to measure the spatial smoothness of the noise, not the anatomy or the activation.

I suggest you leave the detrending order out and let the program decide, also -bmall is overkill, given that you have more than 240 samples in your time series.

A simpler command would be:
SurfSmooth -met HEAT_07 -spec std.SM11_rh.spec \
-surf_A std.rh.smoothwm.asc \
-input v2s_std.rh.RP_run01.niml.dset \
-blurmaster v2s_std.rh.RP_run01.niml.dset \
-output rh.v2s.blr.niml.dset \
-target_fwhm 4 \
-cmask '-a v2s_std.rh.RP_run01.niml.dset -expr bool(a)' \
-detrend_master


cheers,
ziad
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Subject Author Posted

SurfSmooth problem

Chris Ackerman December 31, 2010 03:48AM

Re: SurfSmooth problem

Ziad January 03, 2011 09:24PM

Re: SurfSmooth problem

Chris Ackerman January 04, 2011 10:52AM

Re: SurfSmooth problem

Ziad January 04, 2011 10:32PM

Re: SurfSmooth problem

Ziad January 06, 2011 10:25AM

Re: SurfSmooth problem - Rebuild

bob cox January 06, 2011 10:28AM