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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dharol
July 11, 2009 05:35PM
AFNI experts,

I am starting my first granger causality analysis using Gang Chen's 1dGC in R and am wondering the best way to extract the time series. i have 64 245TR length scans, and am currently using 3dmaskave and looping through all 450 subbriks per subject to generate the time series.

set TR = 0
while (${TR} <245
set roi1 = `3dmaskave -quiet \
-mask ${Mask}'['${maskbrik}']' -mrange 1 1 \
${input}+tlrc'['${TR}']'`
set roi2 = `3dmaskave -quiet \
-mask ${Mask}'['${maskbrik}']' -mrange 2 2 \
${input}+tlrc'['${TR}']'`

echo ${roi1} ${roi2} >> roifile.1D
end

Just wondering if there's a more efficient way to do this?

Thanks for help,
Dharol
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Subject Author Posted

extracting ROI time series for 1dGC

dharol July 11, 2009 05:35PM

Re: extracting ROI time series for 1dGC

rick reynolds July 11, 2009 10:42PM

Re: extracting ROI time series for 1dGC

dharol July 12, 2009 06:02PM