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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December 01, 2014 02:59PM
Hi,
I have a problem using 3dMEMA on surface data.
I have done all the analysis on standard mesh with ld=60. On individual subject, 3dDevonvolve was done to get coef and Tstat for each regressor and the -bucket option was used to save the data. When viewing on individual subject in suma, the result looks very reasonable. I set the AFNI_NIML_TEXT_DATA environment parameter to YES just so that I can also check result in Matlab.

And then I used 3dcopy to copy the "bucket" niml.dset files from different subjects to the same folder to do group analysis. The 3dMEMA command is like this:

3dMEMA -prefix filled.common.groupMEMASurf.$hemi -max_zeros 2 \
-missing_data 0 -model_outliers -set common_resp 02 filled.stats.02.$hemi.niml.dset'[3]' filled.stats.02.$hemi.niml.dset'[4]' \
03 filled.stats.03.$hemi.niml.dset'[3]' filled.stats.03.$hemi.niml.dset'[4]' \
06 filled.stats.06.$hemi.niml.dset'[3]' filled.stats.06.$hemi.niml.dset'[4]' \
07 filled.stats.07.$hemi.niml.dset'[3]' filled.stats.07.$hemi.niml.dset'[4]' \
09 filled.stats.09.$hemi.niml.dset'[3]' filled.stats.09.$hemi.niml.dset'[4]'
$hemi was either lh or rh.
It did run through, but the resulting data was strange. It gave me a .1D file and +orig.HEAD and +orig.HEAD file. Apparently I cannot view the +orig files. I could load the 1D file into suma and there were 4 sub-bricks, the same as what 3dMEMA outputs for volume space data. The activation pattern looks correct, but the statistic parameter (p-value) associated with the t-stat is missing. Also the labels of the sub-bricks are all called "numeric". Reading into the 1D file, it does have ni_stat to label the degree of freedom for the d-stat but this seems to be not read into suma.

I am wondering what would be the correct way to use 3dMEMA for surface data. I tried to convert the "bucket" niml file to binary niml format before processing. But it still comes out the same way.

Thanks!
Mingbo
Subject Author Posted

3dMEMA on surface data

Mingbo December 01, 2014 02:59PM

Re: 3dMEMA on surface data

Peter Molfese December 01, 2014 03:12PM

Re: 3dMEMA on surface data

Mingbo December 01, 2014 03:23PM