fat_proc QC output files

AFNI Message Board
1

Dear Paul and fat_proc users,
I am writing my first afni+fatcat dti pipeline and I found very useful the QC images automatically generated by fat_proc functions, as described in https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/fatcat_prep/GeneralProps.html#automatic-qc-imaging
but in many cases I am not sure to understand from the structured file name the true overlayed images I am looking,… a part some very simple cases and section shown.
It would be nice a more detailed tutorial on QC or more simply a list of output QC file name/description table, in the function --help would be great!
Cheers,
g.c

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Ciao, Giuseppe-

OK, that’s a good idea to have those listed explicitly in the help, I will add those in the near future.

At teh moment, a description of each/most should be listed in the tutorial documentation: after each command example, there is a table of outputs, defining each kind of file output including the images; the descriptions per image are also shown in the captions below the example images, for example scrolling down here:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/fatcat_prep/Prepreprocessing_I.html#fat-proc-convert-dcm-dwis-convert-dwis

I’m also happy to get advice on other kinds of outputs that users think might be useful. The ones done here are just things I thought would be useful from mine own processings.

Thanks,
pt

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Thanks Paul,
[your link] is very useful indeed.
I have another question about fat_proc_grad_plot that I suppose is a QC function too. On my installation linux_openmp_64 (Version AFNI_18.0.11) the function do not work:

$ fat_proc_grad_plot
Traceback (most recent call last):
File “/home/gc/abin/fat_proc_grad_plot”, line 3, in
from mpl_toolkits.basemap import Basemap
ImportError: No module named basemap

must I install something special?
Cheers,
Giuseppe

4

Hi, Giuseppe-

fat_proc_grad_plot is in hyper-beta phase at the moment. Basically, it isn’t really in general consumption for use yet, unfortunately, because I am still sorting out what its outputs will look like, as well as its dependencies (various Python libraries, some of which are kind of annoying to install at the moment). If you have some grad files to visualize, we can discuss that offline, for the time being.

–pt