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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November 28, 2005 11:20AM
Hi,
Here's a typical 3dNLfim command that we normally use:

3dNLfim \
-input input+tlrc.HEAD \
-ignore 0 \
-noise Constant \
-signal GammaVar \
-nconstr 0 -1000.0 1000.0 \
-sconstr 0 0 2 \
-sconstr 1 -1000.0 1000.0 \
-sconstr 2 8 9 \
-sconstr 3 0.15 0.45 \
-nrand 1000 \
-nbest 10 \
-rmsmin 1.0 \
-fdisp 1000.0 \
-bucket 0 output.bucket


Cohen's equation is y=k * (t-t0)^r * exp(-(t-t0)/b)

'-sconstr 0' represents the t0 variable
'-sconstr 1' represents the k variable
'-sconstr 2' represents the r variable
'-sconstr 3' represents the b variable


The command line above is for a dataset with a TR=2s. This means that '-sconstr 0 0 2' ranges from 0s to 4s. These values need to be changed if the TR is say 1sec ('-scontr 0 0 4'). Also the b variable is dependent on TR so if your TR is 1sec, the values need to be doubled: '-sconstr 3 0.3 0.9'. Apart from that there is not much else to worry about.

After trying out a few different values, we chose nrand to be 1000 and nbest to be 10 because it seemed to give good results. This might be an overkill and it takes a while to run but it's better to be safe.

Hope this helps,
Kevin
Subject Author Posted

3dDeconvolve, 3dNLfim, and area under the curve

giuseppe pagnoni November 28, 2005 08:29AM

Re: 3dDeconvolve, 3dNLfim, and area under the curve

Kevin Murphy November 28, 2005 11:20AM

Re: 3dDeconvolve, 3dNLfim, and area under the curve

giuseppe pagnoni November 29, 2005 03:49AM