The --etiv-only option only prints it to the screen and does not create a summary file. The ICV is present in the aseg.stats file and should be present when you run asegstats2table.

If you want to get the single ICV number in a file, you can run

mri_segstats --subject $(filename) --etiv-only | grep atlas_icv| awk '{print $4}' > summaryfile

doug

On 08/15/2013 05:51 PM, charles laidi wrote:

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

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