Are you sure the job was not killed in the middle? The recon-all.log file just stops without a warning or error message. Or does this happen repeatedly?

On 03/07/2016 03:10 PM, Julian Jäckle wrote:

Thank you so much for the response. Unfortunately I am not so familiar with freesurfer but these files do not exist: transforms/talairach_with_skull.lta, brainmask.auto.mgz, brainmask.mgz. I don’t know if it is helpful but below I listed all files which can be found in the subjects directory

_Touch_: talairach.touch, conform.touch

_Scripts_: recon-all-status.log, recon-all.log, recon-all.local-copy, recon-all.env.bak, recon-all.env, recon-all.cmd, IsRunning.Ih+rh, csurfdir, build-stamp.txt

_Mri_: rawavg.mgz, orig_nu.mgz, orig_nu.log, orig.mgz, mri_nu_correct.mni.log.bak, mri_nu_correct.mni.log

   -_Transforms_: 

talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt, talairach_avi_QA.log, talairach_avi.log, talairach.xfm, talairach.auto.xfm

-_Orig_: 001.mgz

-_tmp.mri_nu_correct.mni.12786_: sum.junk, pre-scale.mnc, output.mean.dat, ones.mgz, nu2.mnc, nu2.imp, input.mean.dat

         - 0: template.mnc, nu1_temp.mnc, nu1_residue.mnc, 

nu1_mask.mnc, nu1_log.mnc, nu1_field.mnc, nu1_est.sharp, nu1_est.mnc.temp, nu1_est.mnc, nu1_est.hist, nu1_corr.mnc, nu0.mnc, field_volume.mnc

         - 1: template.mnc, nu2_temp.mnc, nu2_residue.mnc, 

nu2_mask.mnc, nu2_log.mnc, nu2_field.mnc, nu2_est.sharp, nu2_est.mnc.temp, nu2_est.mnc, nu2_est.hist, nu2_corr.mnc, nu1.mnc, field_volume.mnc

(all the other subfolders are empty)

Greetings

Julian

2016-03-07 20:28 GMT+01:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>:

Hi Julian

can you give us more details about what exactly is missing?

cheers
Bruce

On Mon, 7 Mar 2016, Julian Jäckle wrote:


    Dear FS-team


    For purposes of measuring cortical thickness I’ve been running
    recon-all as described on your RecommendedReconstruction site.
    However I am missing some files including e.g the
    skullstripped file. Could you check my log file for the root
    cause?


    Greetings


    Julian




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