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Hi Julia,

For that, you can use the group json file that eddy_squad generates.

You can easily import that in Matlab (using, e.g., https://uk.mathworks.com/matlabcentral/fileexchange/33381-jsonlab-a-toolbox-to-encode-decode-json-files) or in Python (e.g., https://linuxconfig.org/how-to-parse-data-from-json-into-python). Following these approaches, you will generate a structure array or a dictionary, respectively. These will contain all the data and qc metrics that eddy_squad stores and uses to generate the visual group reports. Then, you can easily get the outliers for each metric by computing the means and standard deviations of your group.

All the metrics are stored following the subject order that you have specified in the subject list you passed to eddy_squad.


Hope this helps, cheers,
Matteo

On 11 Mar 2019, at 17:37, Julia Owen <[log in to unmask]> wrote:

Hi,

I've successfully run quad and squad on a large cohort of subjects.  Is there a way to obtain the outliers flagged by running fsl_squad in something like a text file?  Is there also a way to obtain the information graphically displayed in the updated quad reports?  I have so many subjects that it's not feasible for me to look at every one.

Thanks in advance,

-Julia

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