The fix that Anna needs was committed last Friday. Andrew From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Dicamillo, Robert" <rdicami...@mgh.harvard.edu> Reply-To: FS Help <firstname.lastname@example.org> Date: Tuesday, April 10, 2018 at 12:27 AM To: FS Help <email@example.com> Cc: "Dicamillo, Robert" <rdicami...@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=sharing - rob On Apr 9, 2018, at 2:31 PM, Hoopes, Andrew <ahoo...@mgh.harvard.edu<mailto:ahoo...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Anna Daniels <anna.dani...@fu-berlin.de<mailto:anna.dani...@fu-berlin.de>> Reply-To: FS Help <firstname.lastname@example.org<mailto:email@example.com>> Date: Monday, April 9, 2018 at 1:10 PM To: FS Help <firstname.lastname@example.org<mailto:email@example.com>> 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] _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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