Hi Andrew, hi Bruce,

thanks for the tip! Unfortunately, the dev version of mri_normalize did not work (resulted in the same error log) but simply manually checking the control points in the respective cross runs and deleting the ones outside the brain before rerunning worked!

Best, Anna

2018-04-11 23:22 GMT+02:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:

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_DAT

A_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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