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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 . 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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