We don't have a lot of experience running recon-all on windows-ubuntu, but I do know that people do so successfully. It does seem weird that mri_em_register is taking over an hour. Do you have a lot of other things running at the same time? If so, try running with just recon-all

On 10/3/2019 9:09 AM, Троицкий Антон Александрович wrote:

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Hello FreeSurfer Developers,

I have installed the FreeSurfer how described here https://surfer.nmr.mgh.harvard.edu/fswiki/WindowsSupport.

I launch an Ubuntu terminal and stat a freesurfer application from an Ubuntu command line.


I can see in a task manager that different tasks are working and the processing is going.
I can see the output in the ubuntu terminal and see the last steps of processing. 
I don’t know exactly when but after some period of time the processing is freezing and paused. 
It is really strange because I don’t see any task in the task manager associated with the processing of.  It lasts a while and I decide to stop the processing by using ctrl+c. And it is so strange the processing continues after that. It happened twice for the same dataset. 

I have launched the processing of test data  sample-001.nii.gz. It is going well. I have two different datasets that have been processed on the other station and the processing was completed without errors. 

It is an output in recon-all.cmd file

#@# EM Registration Thu Oct  3 09:51:44 MSK 2019                                                                                                                                                                                             
 mri_em_register -rusage /usr/local/freesurfer/subjects/2019-07-22_3DBrainView_T1_2019-10-03_09-18/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/
#@# CA Normalize Thu Oct  3 11:42:10 MSK 2019                                                                                                                                                                                                                                                                                                                                                                                                                                              mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz                                                                                                                                                                                                                                                                                                                                  #--------------------------------------                                                                                                                                                                                                      
#@# CA Reg Thu Oct  3 11:43:49 MSK 2019                                                                                                                                                                                                                                                                                                                                                                                                                                                    mri_ca_register -rusage /usr/local/freesurfer/subjects/2019-07-22_3DBrainView_T1_2019-10-03_09-18/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesu$



Is it normal that the process mri_em_register was going so long? And it continued after I pressed the ctrl+c command. Is it normal this behavior of processing of the data? 
How do you think what is the cause of this kind of behavior of the processing? Does anybody try to do it? I have found this way for parallel processing. https://andysbrainbook.readthedocs.io/en/latest/FreeSurfer/FS_ShortCourse/FS_04_ReconAllParallel.html. But it is not the same.


Best regards,
Anton Troitskii.

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