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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September 05, 2022 06:43PM
Ha, OK (or, as they say in Italy, OK).

Re. the correlation conundrum:

Ah, I see. Indeed, that is a bit tricky. So, you want region-to-voxelwise correlation, not within-network-of-regions correlation? Well, at least 3dNetCorr can output all the time series at once:
-ts_out          :switch to output the mean time series of the ROIs that
                      have been used to generate the correlation matrices.
                      Output filenames mirror those of the correlation
                      matrix files, with a '.netts' postfix.

    -ts_label        :additional switch when using '-ts_out'. Using this
                      option will insert the integer ROI label at the start
                      of each line of the *.netts file created. Thus, for
                      a time series of length N, each line will have N+1
                      numbers, where the first is the integer ROI label
                      and the subsequent N are scientific notation values.

    -ts_indiv        :switch to create a directory for each network that
                      contains the average time series for each ROI in
                      individual files (each file has one line).
                      The directories are labelled PREFIX_000_INDIV/,
                      PREFIX_001_INDIV/, etc. (one per network). Within each
                      directory, the files are labelled ROI_001.netts,
                      ROI_002.netts, etc., with the numbers given by the
                      actual ROI integer labels.
... and it can even do the set of region-to-voxelwise correlation map calculation for you:
-ts_wb_corr      :switch to perform whole brain correlation for each
                      ROI's average time series; this will automatically
                      create a directory for each network that contains the
                      set of whole brain correlation maps (Pearson 'r's).
                      The directories are labelled as above for '-ts_indiv'
                      Within each directory, the files are labelled
                      WB_CORR_ROI_001+orig, WB_CORR_ROI_002+orig, etc., with
                      the numbers given by the actual ROI integer labels.
but I take your point about the role of smoothing in effectively reducing some distortion effects.

Part of me wonders about doing region-to-voxelwise calculations, and then applying a blur to those maps. The correlation process is not linear, so it isn't exchangeable with the linear process of blurring, but probably that would fairly closely approximate having a separate dataset that was blurred and calculating the correlation maps "properly". Unfortunately verifying that hypothesis does the full amount of dual-processing that one would hope to avoid.

Will have to ponder a bit...

--pt
Subject Author Posted

Blurring and 3dNetCorr

dante.picchioni September 04, 2022 02:13PM

Re: Blurring and 3dNetCorr

ptaylor September 04, 2022 03:34PM

Re: Blurring and 3dNetCorr

dante.picchioni September 05, 2022 12:27PM

Re: Blurring and 3dNetCorr

ptaylor September 05, 2022 06:43PM

Re: Blurring and 3dNetCorr

dante.picchioni September 06, 2022 09:33AM