External Email - Use Caution
- Hi there :)
- I am trying to run recon-all on MRI data; I have multiple sequences
including T1 maps and MAGiC. I have tried to run recon-all on these
sequences but get the same error each time:
-
- ERROR: 512, see /tmp/tmp.H88WWu.dcmdjpeg.out for more details
-
- However when looking in that location I only see a H88WWu file, not
H88WWu.dcmdjpeg.out.
- I am using the Ubuntu 18.04 VM with the 7.2.0 release.
-
- Attached is the recon-all.log.
-
- Any suggestions would be very appreciated!
- Thanks
- Beatrice
Mon Sep 5 21:47:40 EDT 2022
cd /home/developer/resmed202200056-PD_MRI_data/BEseg/Anon15
setenv SUBJECTS_DIR /home/developer/resmed202200056-PD_MRI_data/BEseg
/usr/local/freesurfer/7.2.0/bin/recon-all -subject Anon15 -i IM-0010-0001.dcm -all
subjid Anon15
setenv SUBJECTS_DIR /home/developer/resmed202200056-PD_MRI_data/BEseg
FREESURFER_HOME /usr/local/freesurfer/7.2.0
Actual FREESURFER_HOME /usr/local/freesurfer/7.2.0
build-stamp.txt: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
Linux developer-VirtualBox 5.4.0-124-generic #140~18.04.1-Ubuntu SMP Fri Aug 5 11:43:34 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 8192 kbytes
coredumpsize 0 kbytes
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 65536 kbytes
maxproc 31556
maxlocks unlimited
maxsignal 31556
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 7.8G 998M 5.3G 11M 1.5G 6.5G
Swap: 0B 0B 0B
########################################
program versions used
7.2.0 (freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b)
7.2.0
ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:40-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:40-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:40-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:40-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:40-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:40-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:40-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:40-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:40-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:40-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:40-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:40-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:40-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:40-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:40-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:40-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:40-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:40-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:40-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:40-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:40-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:40-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:40-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:40-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:40-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:40-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:40-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:40-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:40-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:41-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:41-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:41-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:41-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:41-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
7.2.0
ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:41-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
7.2.0
ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:41-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:41-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:41-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:41-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:41-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:41-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:41-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:41-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:41-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:41-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:41-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
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ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:41-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:41-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
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ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:41-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
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ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:41-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
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ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:41-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
mri_motion_correct.fsl 7.2.0
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.2.0 TimeStamp: 2022/09/06-01:47:41-GMT BuildTime: Jul 21 2021 02:56:14 BuildStamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b User: developer Machine: developer-VirtualBox Platform: Linux PlatformVersion: 5.4.0-124-generic CompilerName: GCC CompilerVersion: 4.8.5
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
#######################################
GCADIR /usr/local/freesurfer/7.2.0/average
GCA RB_all_2020-01-02.gca
GCASkull RB_all_withskull_2020_01_02.gca
AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
GCSDIR /usr/local/freesurfer/7.2.0/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
#######################################
/home/developer/resmed202200056-PD_MRI_data/BEseg/Anon15
mri_convert /home/developer/resmed202200056-PD_MRI_data/2022_BE_MRIdata/Anon15/Unnamed_15/T1_map_310/IM-0010-0001.dcm /home/developer/resmed202200056-PD_MRI_data/BEseg/Anon15/mri/orig/001.mgz
mri_convert /home/developer/resmed202200056-PD_MRI_data/2022_BE_MRIdata/Anon15/Unnamed_15/T1_map_310/IM-0010-0001.dcm /home/developer/resmed202200056-PD_MRI_data/BEseg/Anon15/mri/orig/001.mgz
reading from /home/developer/resmed202200056-PD_MRI_data/2022_BE_MRIdata/Anon15/Unnamed_15/T1_map_310/IM-0010-0001.dcm...
Starting DICOMRead2()
dcmfile = /home/developer/resmed202200056-PD_MRI_data/2022_BE_MRIdata/Anon15/Unnamed_15/T1_map_310/IM-0010-0001.dcm
dcmdir = /home/developer/resmed202200056-PD_MRI_data/2022_BE_MRIdata/Anon15/Unnamed_15/T1_map_310
Ref Series No = 310
Found 34 files, checking for dicoms
Found 32 dicom files in series.
sh: 1: Syntax error: Bad fd number
First Sorting
Computing Slice Direction
Vs: -0.282501 -0.0976791 4.99106
Vs: -0.0565002 -0.0195358 0.998211
Second Sorting
IsDWI = 0, IsPhilipsDWI = 0
Counting frames
nframes = 1
nslices = 32
ndcmfiles = 32
INFO: applying rescale intercept and slope based on (0028,1052) (0028,1053).
If you do not want this, then set FS_RESCALE_DICOM to 0 and rerun.
PE Dir = ROW (dicom read)
Loading pixel data
JPEG compressed, decompressing
cd /home/developer/resmed202200056-PD_MRI_data/BEseg/Anon15
fsdcmdecompress --i /home/developer/resmed202200056-PD_MRI_data/2022_BE_MRIdata/Anon15/Unnamed_15/T1_map_310/IM-0010-0001.dcm --o /tmp/tmp.H88WWu --jpeg >& /tmp/tmp.H88WWu.dcmdjpeg.out
ERROR: 512, see /tmp/tmp.H88WWu.dcmdjpeg.out for more details
Command exited with non-zero status 1
@#@FSTIME 2022:09:05:21:47:42 mri_convert N 2 e 5.00 S 0.08 U 0.03 P 2% M 8680 F 0 R 874 W 0 c 23 w 890 I 0 O 0 L 0.28 0.12 0.05
@#@FSLOADPOST 2022:09:05:21:47:47 mri_convert N 2 0.33 0.13 0.06
Linux developer-VirtualBox 5.4.0-124-generic #140~18.04.1-Ubuntu SMP Fri Aug 5 11:43:34 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s Anon15 exited with ERRORS at Mon Sep 5 21:47:47 EDT 2022
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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