External Email - Use Caution Hello Lauren:
Open the sR0391178-0002-00001-000208-01.nii.gz file using freeview and see if the whole 3D brain is in place. This should give you a clue as to why this occurred. best, Alan On Wed, Sep 13, 2023 at 1:02 PM Lauren Stephens <laure...@stanford.edu> wrote: > External Email - Use Caution > > Hi Freesurfers, > > I am attempting to run recon-all on a set of .nii.gz files. Each file is > in our subject directory and has run through recon-all. Recon-all only > takes 10 seconds to run and says it was completed without errors. When I > go to the folder recon-all creates, the folders are empty. > > Here is the code we ran: > > recon-all -s 967 -i > /Users/corpuscallosum/Desktop/subjects/sR0391178-0002-00001-000208-01.nii.gz > > Here is the output message: > > Started at Wed Sep 13 10:52:44 PDT 2023 > > Ended at Wed Sep 13 10:52:54 PDT 2023 > > #@#%# recon-all-run-time-hours 0.003 > > recon-all -s 967 finished without error at Wed Sep 13 10:52:54 PDT 2023 > > done > > We are using an iMac Pro 2017 running Ventura 13.5.2 and FreeSurfer > version 7.3.2. > > I have attached the recon-all.log file and would appreciate any > suggestions. We have previously run many successful recon-all's and have > not encountered any issues. > > Thank you, > > Lauren Stephens > > > *Lauren Stephens, MS * > > Assistant Clinical Research Coordinator > > Department of Psychiatry and Behavioral Science > > *Stanford University School of Medicine* > > E: laure...@stanford.edu > > P: (650)-725-1716 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1FAb5I8xYlPAgBt9HJQcYvRJa1vFCwIguqkaqurJoq_3eDr9qIUVDzMBhzeBJOSXcT46BP83fIHRStZ5hk5A-MqjKtQsz-p-qxOFk_quW-9V0AJjPh21OwJM56-e1ZyXCMW77GBznDaM5uxMY5OatiT9p_5D_XvJsakBrfQBZie7kBfBLrl8blwYJEP11fIr8wl2N_xjJ1hSU2NEpxKaU-KPrjLiZMBNkbHLkUHU5Sbkn20B1xjTkjywsRKEWMsEGeNu_QyEdT-kpDfzOUUcvYL1T_6CsBErE1PheBQFEM6hTocEM5ntMidoi8QY97mwY02u24mFoINOu_yxrPtW_1Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > -- *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|* *Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of Neuroscience* *University of Texas, School of Medicine* *Rio Grande Valley* *Texas.*
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