group analysis 101

AFNI Message Board
1

Dear all,
I have a little newbie question for which your feedback would be greatly appreciated:
considering the analysis example in the AFNI_data6 (presented in the online tutorials), how does one get the a file like “OLSQ.FR.betas+tlrc.BRIK” (used in group analysis and present in the folder AFNI_data6/group_results) from the files in the folder AFNI_data6/FT_analysis/FT.results ?
Thank you so much!
Best wishes,
Roxana

2

Hi Roxana,

Here are some options to ponder…

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You can access dataset volumes using the integral index
(zero-based) or using labels (as seen in 3dinfo or the
afni GUI). For example, to extract the response to the
‘pickles’ condition (assuming it is as index 17):

3dbucket -prefix betas.pickles.subj1234 stats.subj1234+tlrc"[17]"

or via labels and a $subj variable name (the full label
for the ‘pickles’ beta is probably pickles#0_Coef):

set subj = subj1234
set cond = pickles
3dbucket -prefix betas.cond.$subj stats.$subj+tlrc"[$cond#0_Coef]"

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Or you could extract them using a long path:

set subj = subj1234
set studydir = /some/path/to/main/study
set subjroot = $studydir/subjects

3dttest++ ....
   subj1234 $subjroot/subj1234.results/stats.subj1234+tlrc"[$cond#0_Coef]"

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Or you could initiate such a command using gen_group_command.py:

gen_group_command.py -command 3dttest++ \
  -dsets $subjroot/subj*.results/stats.subj*+tlrc.HEAD  \
  -subs_betas 'pickles#0_Coef'

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For more info, see the output of:
3dcalc -help
gen_group_command -help

  • rick