Thank you for your email. Yes that v is what freesurfer home is set to. Somehow that GCA file (SMS numerous others) were missing from the averages folder. I manually chopped them from a different 5.3 install, but am not sure v why they are missing (I am the only person using this machine and did not delete anything from the averages folder).
Now that I copied the files over the command I listed runs but crashes with the error mpr2mni305 failed. I get this error on a dataset I have already processed using freesurfer 5.3 centos 6 version without the use-cuda option. Any suggestions would be greatly appreciated. Best wishes, Sal Hi Salil what is FREESURFER_HOME set to? Is it /usr/local/freesurfer? Does /usr/local/freesurfer/average/**RB_all_2008-03-26.gca exist? cheers Bruce On Mon, 8 Jul 2013, Salil Soman wrote: Hi, > Am running this command: > > $FREESURFER_HOME/bin/recon-all -i 3DSPGR.nii.gz -s WCA_248_T1Q_FS > -nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields > -use-cuda -all > > And am get this out put / error: > > Testing for CUDA device: > nvcc: NVIDIA (R) Cuda compiler driver > Copyright (c) 2005-2012 NVIDIA Corporation > Built on Fri_Sep_21_17:28:58_PDT_2012 > Cuda compilation tools, release 5.0, V0.2.1221 > > Driver : 5.50 > Runtime : 5.0 > > Acquiring CUDA device > Using default device > CUDA device: GeForce GTX 660 > > > ======= NUMBER OF OPENMP THREADS = 50 ======= > stable5 > > NVIDIA driver version info: > NVRM version: NVIDIA UNIX x86_64 Kernel Module 319.32 Wed Jun 19 > 15:51:20 PDT 2013 > > ERROR: cannot find /usr/local/freesurfer/average/**RB_all_2008-03-26.gca > > Any suggestions what I am doing incorrectly? > > Thank you, > > Sal > > > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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