Hi guys,

I’m trying to use ‘fslmerge’ and ‘fslmaths -Tmean’ to generate an average volume for nearly 1100 HCP subjects. This obviously requires a lot of RAM, but there is something puzzling that I was wondering if you could shed some light on.

As a test case, to gauge the total memory that I’ll need, I ran the following simple script:

# Merge 101 volumes

fslmerge -t tmpmerge 1[01]*/MNINonLinear/T1w_restore.nii.gz

# Take the mean along the 4th dimension

fslmaths tmpmerge -Tmean tmpmean -odt float

Running that script used a maximum of ~16 GB of memory, even though the tmpmerge.nii.gz file is only ~7 GB.

The gunzipp’ed tmpmerge.nii file is ~8 GB, indicating that the RAM required was double the size of the input to ‘fslmaths’.

Running the two commands separately showed that it is specifically the ‘fslmaths’ command that is the “memory hog” here. Is ‘fslmaths’ pre-allocating memory for an output that is the same size as the input, without regard to the specific operations requested? e.g., In this case, the only operation requested is a “-Tmean”, and thus once the input is loaded, all that should be needed memory wise is a single additional volume (which would be tiny in the scheme of things).

thanks,

-MH

Michael Harms, Ph.D.

-----------------------------------------------------------

Conte Center for the Neuroscience of Mental Disorders

Washington University School of Medicine

Department of Psychiatry, Box 8134

660 South Euclid Ave. Tel: 314-747-6173

St. Louis, MO 63110 Email: [log in to unmask]

The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.