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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Iris Yang
February 16, 2009 04:08PM
Hi Gang,

This is my first time to use ICA tool to process resting state fMRI data. Would you please take a look at the steps I have taken to see whether there is any problem? I am not quite sure whether the pre-processing steps are correct. The other thing is after 3dICA.R how I can create AFNI activation map for each of the components.

Thanks,
Iris

P.S.
#pre-processing raw EPI of a single subject
3dTshift -prefix ts_RestEyeClose+orig RestEyeClose+orig
3dvolreg -dfile mot_tempRestEyeClose -base 'ts_RestEyeClose+orig[163]' -prefix reg_RestEyeClose ts_RestEyeClose+orig
3dmerge -1blur_fwhm 4 -doall -prefix reg_RestEyeClose_blur reg_RestEyeClose+orig
3dcalc -prefix RestEyeClose_mask800 -a 'ts_RestEyeClose+orig[163]' -expr 'astep(a,800)'

#Pre-processing for ICA analysis: dimensionality reduction
3dpc -quiet -mask RestEyeClose_mask800+orig -reduce 10 redim_RestEyeClose -prefix PreICA_RestEyeClose reg_RestEyeClose_blur+orig

adwarp -apar T1Volume+tlrc -dpar 'redim_RestEyeClose+orig' -dxyz 3 -prefix ICAInput_RestEyeClose_dxyz3

# find the components
3dICA.R RestEyeClose_dxyz3_ICAOutput

par.txt file is as below.
Input:ICAInput_RestEyeClose_dxyz3+tlrc
CompOutput: RestEyeClose_dxyz3_ICAOutput
MixOutput:Temp
NoComp:10
Func:logcosh
Type:parallel
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Subject Author Posted

ICA question

Iris Yang February 16, 2009 04:08PM

Re: ICA question

Gang Chen February 17, 2009 10:23AM

Re: ICA question

Iris Yang February 17, 2009 01:00PM

Re: ICA question

Irist Yang February 18, 2009 11:03AM

Re: ICA question

Gang Chen February 18, 2009 01:54PM

Re: ICA question

Iris Yang February 18, 2009 02:11PM

Re: ICA question

Gang Chen February 18, 2009 03:56PM

Re: ICA question

Iris Yang February 19, 2009 10:59AM