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

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-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]