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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Steve Greening
March 04, 2010 04:59PM
Hi Gang,

I am trying to set up the individual participant time series files (with 2 ROIs) for running with the SEMscript.csh. I created the script below, and it appears to work. I just wanted to verify that everything seems reasonable.
One thing you'll notice is that I have re-run deconvolve to get the -cbucket output because I didn't include it initially.

Cheers,
Steve


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3dUndump -prefix 6mmAmysphere -master groupbain_n16+tlrc -xyz -dval 1 -srad 6 ROIspheresAmy
3dUndump -prefix 6mmRmPFCsphere -master groupbain_n16+tlrc -xyz -dval 1 -srad 6 ROIspheremPFC

3dresample -master FeAwareVnoAware_N16+tlrc -prefix 6mmAmysphere.r -inset 6mmAmysphere+tlrc
3dresample -master FeAwareVnoAware_N16+tlrc -prefix 6mmRmPFCsphere.r -inset 6mmRmPFCsphere+tlrc

3dDeconvolve -input pb04.1028*warp+orig.BRIK .... -bucket SEMdecon -cbucket cSEMdecon -x1D SEMdecon

3dSynthesize -cbucket cSEMdecon+orig -matrix SEMdecon.xmat.1D -select baseline -select polort -select FD_F FD_B DN_D DN_N DN_B FN_F FN_B D_D F_F N_N Er Blank -prefix 1028SEMfearsuppEONI

3dTcat -prefix 1028.SEMbasedata pb04.1028.r01.warp+orig pb04.1028.r02.warp+orig pb04.1028.r03.warp+orig pb04.1028.r04.warp+orig pb04.1028.r05.warp+orig pb04.1028.r06.warp+orig

3dcalc -a 1028SEMfearsuppEONI+orig -b 1028.basedata+orig -expr b-a -prefix 1028.SEM.FearSup

adwarp -dxyz 2 -apar /media/Linux/BR_RT_locked/1028/1028.results/BR_1028_192.ANATwarp+tlrc -dpar 1028.SEM.FearSup+orig -prefix 1028.SEM.FearSup

3dmaskave -mask 6mmAmysphere.r+tlrc -mrange 1 1 1028.SEM.FearSup+tlrc > 1028.FSup.AMY.ts.1D
3dmaskave -mask 6mmRmPFCsphere.r+tlrc -mrange 1 1 1028.SEM.FearSup+tlrc > 1028.FSup.mpfc.ts.1D

1dcat 1028.FSup.AMY.ts.1D 1028.FSup.mpfc.ts.1D > 1028.FSup.1D

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Subject Author Posted

Time Series Extraction for SEM/PATH

Steve Greening March 04, 2010 04:59PM

Re: Time Series Extraction for SEM/PATH

Gang Chen March 05, 2010 12:37PM

Re: Time Series Extraction for SEM/PATH

Steve Greening March 05, 2010 04:34PM

Re: Time Series Extraction for SEM/PATH

Steve Greening March 06, 2010 10:51AM