Do you mean that I should have used higher memory?

Is there a way to continue running it from where it stopped or should I start it all over again?

On the Freesurfer Archive there's a suggestion to use the following command: recon-all -make all -s <subjid> However, when I tried it gave an error; ERROR: cannot find /share/apps/freesurfer/6.0.0/subjects/103T.

On Thu, Aug 2, 2018 at 12:49 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

hmmm, it looks like it just stopped in the middle of a process. DId it exceed some wall time limit perhaps?

On Thu, 2 Aug 2018, Ortal Nakash wrote:

        External Email - Use Caution        

Sure, here it is.

On Thu, Aug 2, 2018 at 12:40 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
      can you send it as a text file (not converted to .docx)?
      On Thu, 2 Aug 2018, Ortal Nakash wrote:


                    External Email - Use Caution        

            I copied it in the attached file.
            Thank you,
            Ortal

            On Thu, Aug 2, 2018 at 12:23 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
            wrote:
                  Hi Ortal

                  you need to send us the recon-all.log, otherwise we don't have the
            information we need
                  to help you

                  cheers
                  Bruce
                  On Thu, 2 Aug 2018, Ortal Nakash wrote:


                                External Email - Use Caution        

                        Hi,

                        I tried to run the recon-all command on a single participant on
            a high
                        memory cluster by typing:

                        qlogin -q qlogin.himem.q -l h_vmem=20G,s_vmem=20G


                        recon-all -i 103_T1.nii.gz -s 103T -sd
                        /data/jag/cnds/ortal/freesurftest/C103/ -all


                        - Most of the necessary files were created, however the
            aparc.a2009 files
                        and the recon-all.done
                        file were not.


                        sincerely,

                        Ortal Nakash



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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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