Dear Freesurfers,
I have a problem using the "mri_segstats" function. I'm trying to get Intra cranial volumes (ICV) from images that I have previously segmented. As I have lots of images, I'm using this script :
" foreach filename (*_conv) mri_segstats --subject $(filename) --etiv-only --sum summaryfile end "
The script is working very well except for the -sum option : I'm not able to find the summary file in my directory : the ICV are printed in my Terminal but I don't get all the ICV in a summary file. My ultimate goal is to import the ICV in an excel sheet...
My question is : where can I find the summary file ? Should I specify after the -sum option an existing text file ? I don't understand how the -sum option works. Is there a function, like in "asegstats2table", that allows to directly get all the output of mri_segstats in a table ?
I wasn't able to find an answer to my question in freesurfer wiki or in the mailing list messages.
Thanks a lot for your attention,
Best regards,
Charles