p.s. you probably want to grab a new freeview also, as it lets you jump to the voxel coords of each control point so you can see them On Wed, 11 Apr 2018, Hoopes, Andrew wrote:

Hi Anna,


You can download the new mri_normalize from this link -


To get it into your FS installation, first set executable permissions and then 
move it into your
$FREESURFER_HOME/bin directory (sudo might be required):


chmod +x /path/to/downloaded/mri_normalize

mv /path/to/downloaded/mri_normalize ${FREESURFER_HOME}/bin/





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


Hi Bruce,

thank you for the quick reply!

Ubuntu 16.04 LTS 64-bit


Please let me know how to incorporate the new version into the installation.

Thank you very much and best,


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


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 
> 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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