The fix that Anna needs was committed last Friday.
Andrew

From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Dicamillo, Robert" 
<rdicami...@mgh.harvard.edu>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, April 10, 2018 at 12:27 AM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Cc: "Dicamillo, Robert" <rdicami...@mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all: exited with errors (white matter peak at 
110, cannot allocate memory)

If you are running on Ubuntu, I have a build of the freesurfer source checked
out from about one month ago (March 9th) that I did on an Ubuntu 16.04 system 
using gcc 4.9.

However,  I did not have the test data to run tests, so I must add the 
disclaimer that the binaries
have not gone thru the usual tests.  But if you want to try it, you can download
the compressed ~2G archive from the link below.  It is an archive of the 
./install
tree with ./bin, ./lib, etc.

https://drive.google.com/file/d/1hWs3gdfVExRMW5nl-aufQyMX8yWSHi8Y/view?usp=sharing

- rob

On Apr 9, 2018, at 2:31 PM, Hoopes, Andrew 
<ahoo...@mgh.harvard.edu<mailto:ahoo...@mgh.harvard.edu>> wrote:

Hi Anna,

Unfortunately, we’re not able to build the dev code right now due to a compile 
error, but this should get sorted out within the next day or two, so I can help 
you out with getting this new mri_normalize then

best
Andrew

From: 
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Anna Daniels 
<anna.dani...@fu-berlin.de<mailto:anna.dani...@fu-berlin.de>>
Reply-To: FS Help 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, April 9, 2018 at 1:10 PM
To: FS Help 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] recon-all: exited with errors (white matter peak at 
110, cannot allocate memory)

Hi Bruce,
thank you for the quick reply!
Ubuntu 16.04 LTS 64-bit
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Please let me know how to incorporate the new version into the installation.
Thank you very much and best,
Anna


Hi Anna

no attachments :<

Srishti's issue stemmed from control points outside of the head. The
current (dev) version of mri_normalize detects and removes them. Can you
grab a new version of mri_normalize and see if it fixes your problem? Let
us know your hardware/software environment and we will get it to you

cheers
Bruce


On Fri, 6 Apr 2018, Anna Daniels wrote:

> Hi Bruce, hi Srishti,
>
> I have exactly the same problem with several subjects rerunning recon-all
> and there was sufficient memory available. I also tried out the last command
> directly which resulted in the same error log.
>
> ?mri_normalize 
> -f/home/anna/FREESURFER/00_DATA_MABT1T2/02a_MABT1T2_cross_edits_transfer/rrer
> uncrosstest_cp17/22275_T1_fs_edit/tmp/control.dat -mprage -aseg
> aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz
>
> Attached you can find the input file.
>
> Thank you and best,
> Anna?[icon_10_generic_list.png] ?22275_T1_fs_edit.zip[IMAGE]
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