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

gt;> best >> >> Andrew >> >> >> >> From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Anna Daniels >> <anna.dani...@fu-berlin.de> >> Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu> >> Date: Monday, April 9, 201

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

vard.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

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

rvard.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-c

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

7 AM To: FS Help <freesurfer@nmr.mgh.harvard.edu> 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 o

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

esurfer@nmr.mgh.harvard.edu>> Date: Monday, April 9, 2018 at 1:10 PM To: FS Help <freesurfer@nmr.mgh.harvard.edu<mailto: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 f

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

f Anna Daniels <anna.dani...@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

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

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

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

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

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_

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

can you email us the input file and the full command line you ran? On Thu, 5 Apr 2018, srishti goel wrote: So it gave this error: 3d normalization pass 1 of 2 white matter peak found at 110 HISTOalloc(-2147483648): could not allocate histogram Cannot allocate memory Best, Srishti

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

So it gave this error: 3d normalization pass 1 of 2 white matter peak found at 110 HISTOalloc(-2147483648): could not allocate histogram Cannot allocate memory Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at

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

let's see if it works. If it does, you should be able to run recon-all -s SUBJID -make all cheers Bruce On Thu, 5 Apr 2018, srishti goel wrote: Should I re-run the recon-all after running the last command from recon-all.cmd? Best, Srishti Social/Clinical Research Specialist Child Imaging

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

Should I re-run the recon-all after running the last command from recon-all.cmd? Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 On Thu, Apr 5,

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

Hi Srishti if you look in the subject's scripts dir there should be a file named "recon-all.cmd". Try rerunning the last command in it (probably from the mri dir) cheers Bruce On Thu, 5 Apr 2018, srishti goel wrote: I am sorry, I am not sure what do you mean by running the command line

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

I am sorry, I am not sure what do you mean by running the command line directly? I use the following command: sbatch --mem 2200 -t 6-00:00 --mail-type END --mail-user srish...@email.unc.edu --wrap "export SUBJECTS_DIR=/proj/hng/sheridanlab/freeSurfer/DukeYAS/Freesurfer_out/; recon-all -s 13166

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

if you run the command that failed again on the command line directly (that is, not in recon-all) does it fail again? On Thu, 5 Apr 2018, srishti goel wrote: Hi Bruce, The machine definitely hasn't run out of memory. Here is the memory usage from recon-all.log                        total  

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

Hi Bruce, The machine definitely hasn't run out of memory. Here is the memory usage from recon-all.log total usedfree shared buff/cache available Mem: 26372696834330048 152102696 1294477294224 191963372 Swap: 2097148

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

Hi Srishti are you sure that your machine didn't just run out of memory? The recon-all.log file includes the amount of free (and total) memory at the time the process was started. cheers Bruce On Thu, 5 Apr 2018, srishti goel wrote: Hi, I have been trying to edit structural brains and

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

Hi, I have been trying to edit structural brains and very few times I would get the following error while running recon-all -s subjID white matter peak found at 110 cannot allocate memory Upon looking at the archive, there was only one similar issue and it was recommend to check mri_info as the