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UNCDEPENdLab / fmri.pipeline

R package for running full fMRI GLM analyses in FSL and other software.
GNU General Public License v3.0
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Rename zstat references to contrast names? #3

Closed wasciutto closed 1 year ago

wasciutto commented 1 year ago

It's always bugged me that fsl by default names its files like zstat[index] instead of using the actual name of the contrast, forcing the user to pull up a reference of which zstat index goes with each contrast when glancing through fsl's output:

image image image

If it's possible to change this within the fsf files (not sure), we could take advantage of our opportunity to name these files according to contrast, for example:

image

Of course, there may be a good reason for using zstat[index] that I am not aware of - maybe zstat is meant to represent a more generic example that just contrast, for example. Also, again may not be possible due to it being non-configurable in the template files.

wasciutto commented 1 year ago

Update: noticed that L3 names its files as requested here for L1

michaelhallquist commented 1 year ago

Thanks, Will. The problem you name bugs me as well. Overall, I don't think it's a good idea to alter the names of FSL outputs since downstream programs (including some within FSL) make assumptions about the structure.

I wrote the combine_feat_l3_to_afni with this problem in mind. That function gives the user substantial flexibility in how FEAT group outputs are structured, assembling them into BRIK/HEAD files that can be loaded into AFNI, which I think does a better job of helping the user flip through and compare many maps.

Perhaps we could think of a similar extension on the FSL side (e.g., structuring custom folder outputs). Open to input on this.

wasciutto commented 1 year ago

Closing due to Michael's feedback above