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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ptaylor
September 21, 2020 09:37PM
Hi, Freya-

Sure, we have the technology!

If this is an example of running 3dNetCorr on the full time series (some made up names here, to protect the innocent dsets): 
3dNetCorr                                       \
    -inset FMRI_DSET.nii.gz                 \
    -in_rois ROI_MAP.nii.gz                  \
    -fish_z                                     \
    -prefix o.full                   \
... then here is an example of selecting "just" the first 600 time points from the input FMRI dset: 
3dNetCorr                                       \
    -inset FMRI_DSET.nii.gz'[0..599]'                   \
    -in_rois ROI_MAP.nii.gz                  \
    -fish_z                                     \
    -prefix o.part                   \

This is using the "subbrick selector" functionality in AFNI. If you run this command to open the given afni_handout: 
afni_open -aw afni30_vol_dset_basics.pdf
... then go to PDF page 24 for more examples. Note: Some kind of quotes around the square brackets is necessary, because otherwise the Linux shell will try to interpret those as its own special characters.

Note also that AFNI uses zerobased counting, so that the "first" volume in a dset is actually volume [0]. This is in line with programming languages like C and Python. (Soooorrrry Matlab and R users :(....)

--AFNI person "pt"
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Subject Author Posted

3dNetCorr On Subset of the Time Series

NegativePotato September 15, 2020 11:27AM

Re: 3dNetCorr On Subset of the Time Series

ptaylor September 21, 2020 09:37PM