I don't think you'll need to run the surfaces again. --no-aseg is passed to make_average_volume from make_average_subject.
Ruchika Shaurya Prakash wrote:
I just downloaded the latest version last week. Is there a change since then? Also, I get the --no-aseg option with make_average_volume and not with make_average_subject - but I am thinking that is probably okay since the surfaces are already done. Do you think that I need to run the surfaces again?
Thanks, -Ruchika.
---- Original message ----
Date: Tue, 27 Jan 2009 15:01:20 -0500 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] possible memory allocation problem -
make_average_volume
To: Ruchika Shaurya Prakash rprakash@uiuc.edu Cc: freesurfer@nmr.mgh.harvard.edu
Sorry, just run it with --no-aseg (for that you may need a new version). It probably ran the surfaces ok and then bonked on the volumes (and probably only on the aseg).
doug
Ruchika Shaurya Prakash wrote:
I do have this option - but that would mean that I would not get the average for volumes?
Also, if you take a look at the make_average_surface.log - that got completed without any problems. So do I need to run the make_average_subject command again?
Thanks, -Ruchika.
On Jan 27, 2009, at 1:34 PM, Douglas N Greve wrote:
Try running it with --no-vol. If you don't have this option, then you may need to upgrade.
Ruchika Shaurya Prakash wrote:
Hello
I am running the make_average script on 92 Ss and get the following error message: nframestat = 92 Allocating output mri_concat (63810) malloc: *** mmap(size=262144) failed (error code=12) *** error: can't allocate regions *** set a breakpoint in malloc_error_break to debug MRIalloc (256, 256, 256): could not allocate 262144 bytes for 13929th slice
Following some of the threads, it seems like the problem is in averaging the volumes and Doug had provided some scripts in the following location, the link to which is not working anymore: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Would it be possible to put the files back? I am using freesurfer v. 4.1.0 and am attaching the make_average_surface.log and make_average_volume.log files, in case there are some other issues. Thanks for your help!
-Ruchika. =
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Douglas N Greve