The fix that Anna needs was committed last Friday. Andrew

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Dicamillo, Robert" RDICAMILLO@mgh.harvard.edu Reply-To: FS Help freesurfer@nmr.mgh.harvard.edu Date: Tuesday, April 10, 2018 at 12:27 AM To: FS Help freesurfer@nmr.mgh.harvard.edu Cc: "Dicamillo, Robert" RDICAMILLO@mgh.harvard.edu Subject: Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

If you are running on Ubuntu, I have a build of the freesurfer source checked out from about one month ago (March 9th) that I did on an Ubuntu 16.04 system using gcc 4.9.

However, I did not have the test data to run tests, so I must add the disclaimer that the binaries have not gone thru the usual tests. But if you want to try it, you can download the compressed ~2G archive from the link below. It is an archive of the ./install tree with ./bin, ./lib, etc.

https://drive.google.com/file/d/1hWs3gdfVExRMW5nl-aufQyMX8yWSHi8Y/view?usp=s...

- rob

On Apr 9, 2018, at 2:31 PM, Hoopes, Andrew <AHOOPES@mgh.harvard.edumailto:AHOOPES@mgh.harvard.edu> wrote:

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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Anna Daniels <anna.daniels@fu-berlin.demailto:anna.daniels@fu-berlin.de> Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, April 9, 2018 at 1:10 PM To: FS Help <freesurfer@nmr.mgh.harvard.edumailto: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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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]