help > RE: Skull extracted denoised output
Aug 2, 2020  11:08 AM | Alfonso Nieto-Castanon - Boston University
RE: Skull extracted denoised output
Hi Panos,

That is likely the effect of masking with the "analysis mask" (a general brainmask defined in Setup.Options), rather than explicitly a skull removal step. I would perhaps suggest to change the analysis mask option to either no-masking, or some larger / more liberal explicit mask? (this would require to re-run Setup and Denoising steps)

If you prefer to create an alternative denoised dataset just for 'out-of-CONN' analyses, but without changing or having to redo or affect any of your current CONN analyses, you may also do that as:

1) open your CONN project, and manually create a new secondary dataset (in 'Setup.functionals', select 'primary dataset', and then select in the same menu 'new'; if you want, select then the 'label' option in the same menu and give this new dataset a name/label -e.g. "external" without the quotes)

2) run the command:

   'Setup.preprocessing.sets', 'external',...                          % change this to the label or number of your new secondary dataset
   'Setup.preprocessing.steps', {'functional_regression', 'functional_bandpass'}, ...
   'Setup.preprocessing.reg_names', {'realignment','scrubbing','White Matter','CSF'}, ...
   'Setup.preprocessing.reg_dimensions',[inf, inf, 5, 5], ...   % change this to modify the options for this denoised dataset
   'Setup.preprocessing.reg_deriv', [1, 0, 0, 0], ...               % change this to modify the options for this denoised dataset
   'Setup.preprocessing.bp_filter', [0.008 inf])                     % change this to modify the options for this denoised dataset

That will create a new set of functional files (named bdswau*.nii) containing the denoised and band-passed functional data. Since these are stored as a secondary dataset they will not affect any of your existing analyses (also since this step is run as a preprocessing step it will not be masked at all). Last, you may also modify the denoising options above if you feel that the 'out-of-CONN' analyses would benefit from different denoising settings.

Hope this helps
Originally posted by Panos Fotiadis:
Hi Alfonso,

Hope all is well! I analyzed my resting state fMRI scans using the default pre-processing pipeline (output in MNI space) and, at the end, saved the denoised dswau* file. I noticed that compared to the swau* file, dswau* seems to be skull extracted and in a few of my subjects there was a very small number of brain matter voxels that had consequently been removed, particularly in the occipital regions. A few questions that I had were:

1) Since I'm performing some analyses where I'm looking into the BOLD signal along the whole cortical ribbon (including the BOLD values of those removed voxels), I was wondering if there was a way to save the dswau* file but with the skull included (for instance by potentially commenting out the code that applies the skull removal)? Or is the skull removal an essential step for the calculation of the BOLD signal and the creation of the dswau* file?

2) If (1) is possible, should I just re-run the denoising step (which should overwrite everything?), or should I run the pipeline from the beginning?

Thanks in advance for all the help!


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Panos Fotiadis Jul 24, 2020
RE: Skull extracted denoised output
Alfonso Nieto-Castanon Aug 2, 2020
Panos Fotiadis Aug 4, 2020
Alfonso Nieto-Castanon Aug 12, 2020
Panos Fotiadis Aug 12, 2020
Alfonso Nieto-Castanon Aug 12, 2020
Panos Fotiadis Aug 13, 2020
Panos Fotiadis Aug 2, 2020