Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

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_...

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]