Re: [Freesurfer] recon-all -s exited with ERRORS

@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] recon-all -s exited with ERRORS It looks like there are a lot of defects as I see a lot of these messages An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. This may cause recon-all to run

Re: [Freesurfer] recon-all -s exited with ERRORS

It looks like there are a lot of defects as I see a lot of these messages An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. This may cause recon-all to run very slowly or crash. if so, see https://surfer.nmr.mgh.harvard.e

[Freesurfer] recon-all -s exited with ERRORS

External Email - Use Caution Hi, FreeSurfer Developers, I am attempting to use the recon-all to reconstruction, I successfully run this command in some subjects, but it also failed in around 1/3 of subjects. And after running the recon-all of this 1/3 subjects. It will show “

Re: [Freesurfer] recon-all -s exited with ERRORS

How long does it take to run the test? Thanks, Leo Souza From: Pedro Paulo de Magalhães Oliveira Junior [mailto:p...@netfilter.com.br] Sent: Monday, June 13, 2011 6:20 PM To: Leo Souza Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all -s exited with ERRORS recon-all -s bert

Re: [Freesurfer] recon-all -s exited with ERRORS

recon-all -s bert -all -use-gpu -- iOS 4.3 Em 13/06/2011, às 21:30, Leo Souza escreveu: /recon-all -use-gpu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in th

Re: [Freesurfer] recon-all -s exited with ERRORS

-use-cuda is invalid I think, but I did -use-gpu and see what I get: [root@cuda-final2 bin]# ./recon-all -use-gpu Testing for CUDA device: nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2010 NVIDIA Corporation Built on Thu_Nov__4_12:44:17_PDT_2010 Cuda compilation tools, release 3.2, V0

Re: [Freesurfer] recon-all -s exited with ERRORS

Okay, Let me see what's gonna happen. Thanks, *Leo Souza* On 06/13/2011 04:10 PM, Douglas N Greve wrote: Try adding -use-cuda to recon-all Leo Souza wrote: Yes, I did that, but it doesn't actually uses the GPU to do that, only CPU. GPU percentage is 0%. (you can check it by do running: "nvi

Re: [Freesurfer] recon-all -s exited with ERRORS

Try adding -use-cuda to recon-all Leo Souza wrote: > Yes, I did that, but it doesn't actually uses the GPU to do that, only > CPU. > > GPU percentage is 0%. (you can check it by do running: "nvidia-smi -q > -d UTILIZATION -l 3" if your'e using any recent drivers. > > > Thanks, > *Leo Souza* > >

Re: [Freesurfer] recon-all -s exited with ERRORS

Sorry my typos, got a weird keyboard here. Thanks, *Leo Souza* On 06/13/2011 03:27 PM, Leo Souza wrote: Yes, I did that, but it doesn't actually uses the GPU to do that, only CPU. GPU percentage is 0%. (you can check it by do running: "nvidia-smi -q -d UTILIZATION -l 3" if youŕe using any r

Re: [Freesurfer] recon-all -s exited with ERRORS

Yes, I did that, but it doesn't actually uses the GPU to do that, only CPU. GPU percentage is 0%. (you can check it by do running: "nvidia-smi -q -d UTILIZATION -l 3" if your'e using any recent drivers. Thanks, *Leo Souza* On 06/13/2011 02:44 PM, Douglas N Greve wrote: When you run recon-a

Re: [Freesurfer] recon-all -s exited with ERRORS

When you run recon-all, it will create a recon-all-status file in the scripts directory. This has the start times of all the processes, so you can work out how long each took. This will be wall clock time, so take that into account. doug Leo Souza wrote: > Hi Carolina, > > Do you know how can

Re: [Freesurfer] recon-all -s exited with ERRORS

Hi Carolina, Do you know how can I run Freesurfer just to get some Benchmark Numbers and to Check GPU Performance using Cuda? Thanks, *Leo Souza* On 06/13/2011 07:04 AM, Carolina Valencia wrote: Thanks a lot, it works. just waiting 24 hours. Best regards, Carolina 2011/6/10

Re: [Freesurfer] recon-all -s exited with ERRORS

Thanks a lot, it works. just waiting 24 hours. Best regards, Carolina 2011/6/10 > Hi Carolina, > > Sorry My bad. I was inaccurate in my previous message. > > -subject should work. > > Assuming that the MPRAGE of your subject is under the following directory: > > /freesurfer/subjects/buckner_da

Re: [Freesurfer] recon-all -s exited with ERRORS

Hi Carolina, Sorry My bad. I was inaccurate in my previous message. -subject should work. Assuming that the MPRAGE of your subject is under the following directory: /freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig set your SUBJECTS_DIR to /freesurfer/subjects/buckner_data/tuto

Re: [Freesurfer] recon-all -s exited with ERRORS

Hi Carolina, -subject is not recognized by Freesurfer...Use -subjid or -s instead. setenv SUBJECTS_DIR recon-all -all -i /MPRAGE.nii.gz -s /hptu_subj001 Priti > Hello Freesurfer's users, > > I'm starting using FS and I have a problem running recon-all > I create a folder called hptu_subj001 w

[Freesurfer] recon-all -s exited with ERRORS

Hello Freesurfer's users, I'm starting using FS and I have a problem running recon-all I create a folder called hptu_subj001 which contains MPRAGE.nii.gz within tutorial_subj First I convert nii.gz to mgz qith the command: recon-all -i MPRAGE.nii.gz -s hptu_subj001 and then in order to process all