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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Timothy Souza
August 07, 2003 11:54AM
Doug,

Ok, I think we figured out what is going on with this dataset! It is the sequence of events in which we pre-process which causes 3dDeconvolve to see this dataset as non "slice-tshifted" Basically, we perform the following steps in AFNI.

to3d
3dTshift
3dvolreg

--> at this point (which I forgot to mention in my earlier post), we are using FSL to register our MPRAGE and EP datasets in to MNI 152 T1. We then bring these MNI normalized datasets back into AFNI, which we then gaussian blur and submit to 3dDeconvolve.

So 3dTshifted EPs are converted to ANALYZE format, normalized in FSL, and to3d is run again to create AFNI datasets from the ANALYZE format. This AFNI dataset has no markings on it that identify it as having slice-times set to 0. So basically, I guess we are looking for a way to have 3dDeconvolve ignore the fact that there isn't such a tag in this dataset.

Thanks!
Tim Souza
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Subject Author Posted

3dTshift and -stim_nptr usage

Timothy Souza August 06, 2003 11:59AM

Re: 3dTshift and -stim_nptr usage

B. Douglas Ward August 06, 2003 05:29PM

Re: 3dTshift and -stim_nptr usage

Timothy Souza August 07, 2003 09:39AM

Re: 3dTshift and -stim_nptr usage

B. Douglas Ward August 07, 2003 10:50AM

Re: 3dTshift and -stim_nptr usage

Timothy Souza August 07, 2003 11:54AM

Re: 3dTshift and -stim_nptr usage

B. Douglas Ward August 07, 2003 01:14PM

Re: 3dTshift and -stim_nptr usage

Timothy Souza August 07, 2003 01:17PM

Re: 3dTshift and -stim_nptr usage

Tom Ross August 07, 2003 01:17PM