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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Will Foran
January 25, 2018 01:28PM
I imagine there is an easier way to make a mask for a p-value threshold given an f-stat subbrick.

Our strategy is to extract the statpar of the brick and use that with fift_t2p. I think we could also use e.g. stat2cdf(0.05,4,$ab,0) or cdf -p2t fift .005 14 882 | sed 's/t = //'.

Either way it seems like we are tripping over ourselves to extract and feed back data 3dcalc might already know -- the stat parameters of the subbrik it is working on. 


3dinfo $file'[5]'
#     ...
#     -- At sub-brick #0 'SEScomp:Time F' datum type is short:            0 to         32767 [internal]
#                                            [*   0.00015631]             0 to       5.12182 [scaled]
#     statcode = fift;  statpar = 14 882
#     ...

ab=$(3dinfo -verb $file"[5]"|
       perl -lne 'print join(",", split(/\W+/,$1)) if m/statpar = (.*)/')
#      14,882

 # calc mask: lower pval (converted from f) than threshold
 3dcalc \
       -prefix mask.nii.gz \
       -f $file"[5]" \
       -expr "step(  0.05 - fift_t2p(f,$ab) )" \
       -overwrite \
       -datum short
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Subject Author Posted

f to p in 3dcalc

Will Foran January 25, 2018 01:28PM

Re: f to p in 3dcalc

discoraj January 26, 2018 12:40PM