You did TBSS? You could save one loop by running the command on the all_FA image then, no?
> On Mar 3, 2016, at 3:03 AM, Matthew Webster <[log in to unmask]> wrote:
>
> Hello,
> In this case, Michael's answer above is the one to use - you just need two for loops to go over the subjects and ROIs, using the filenames as the basename for the text file.
>
> Kind Regards
> Matthew
>
>> Thanks for your responses guys! Indeed as [log in to unmask] said, I want to automate the process of finding mean FA for one scan and one ROI. I already have a mean_FA map which was generated by the TBSS process, however that doesn't represent the mean_FA values for a single patient.
>>
>> Any ideas on what code to use in order to automate the "fslmeants -i subject_FA_map.nii.gz -m ROI_mask -o subject_mean_FA_ROI.txt" command would be greatly appreciated.
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