External Email - Use Caution 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. [cid:4348455d-9967-4416-9824-c67b83e00ac4@fccho-moscow.ru] 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.
#--------------------------------- # New invocation of recon-all Thu Oct 3 09:18:22 MSK 2019 mri_convert /home/FreeSurferData/164753_Ogarkov/2019-07-22_3DBrainView_T1/CN90840/801/00010001 /usr/local/freesurfer/subjects/2019-07-22_3DBrainView_T1_2019-10-03_09-18/mri/orig/001.mgz #-------------------------------------------- #@# MotionCor Thu Oct 3 09:20:21 MSK 2019 cp /usr/local/freesurfer/subjects/2019-07-22_3DBrainView_T1_2019-10-03_09-18/mri/orig/001.mgz /usr/local/freesurfer/subjects/2019-07-22_3DBrainView_T1_2019-10-03_09-18/mri/rawavg.mgz mri_convert /usr/local/freesurfer/subjects/2019-07-22_3DBrainView_T1_2019-10-03_09-18/mri/rawavg.mgz /usr/local/freesurfer/subjects/2019-07-22_3DBrainView_T1_2019-10-03_09-18/mri/orig.mgz --conform mri_add_xform_to_header -c /usr/local/freesurfer/subjects/2019-07-22_3DBrainView_T1_2019-10-03_09-18/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/2019-07-22_3DBrainView_T1_2019-10-03_09-18/mri/orig.mgz /usr/local/freesurfer/subjects/2019-07-22_3DBrainView_T1_2019-10-03_09-18/mri/orig.mgz #-------------------------------------------- #@# Talairach Thu Oct 3 09:21:58 MSK 2019 mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Oct 3 09:24:37 MSK 2019 talairach_afd -T 0.005 -xfm transforms/talairach.xfm awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /usr/local/freesurfer/subjects/2019-07-22_3DBrainView_T1_2019-10-03_09-18/mri/transforms/talairach_avi.log tal_QC_AZS /usr/local/freesurfer/subjects/2019-07-22_3DBrainView_T1_2019-10-03_09-18/mri/transforms/talairach_avi.log #-------------------------------------------- #@# Nu Intensity Correction Thu Oct 3 09:24:38 MSK 2019 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 mri_add_xform_to_header -c /usr/local/freesurfer/subjects/2019-07-22_3DBrainView_T1_2019-10-03_09-18/mri/transforms/talairach.xfm nu.mgz nu.mgz #-------------------------------------------- #@# Intensity Normalization Thu Oct 3 09:27:44 MSK 2019 mri_normalize -g 1 -mprage nu.mgz T1.mgz #-------------------------------------------- #@# Skull Stripping Thu Oct 3 09:29:58 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.skull.dat -skull nu.mgz /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta mri_watershed -rusage /usr/local/freesurfer/subjects/2019-07-22_3DBrainView_T1_2019-10-03_09-18/touch/rusage.mri_watershed.dat -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# 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/talairach.lta #-------------------------------------- #@# 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/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z
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