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 -
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/centos6_x86_64/mri_normalize

 

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/

 

best

Andrew

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Anna Daniels <anna.daniels@fu-berlin.de>
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
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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