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Dear freesurfer team,
I just tried to run recon-all on my T1 weighted images with the new freesurfer
8 version, but unfortunately the analysis stops with an error (it worked
without any error using freesurfer 7). I've searched the list and no similar
errors have been reported. Does anyone have any thoughts on how to
trouble-shoot this one?
the following problem occurred with image
/bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig.mgz
:
Traceback (most recent call last):
File "/bif/software/FREESURFER/freesurfer-8.0.0/python/scripts/mri_synthseg",
line 324, in predict
image, aff, h, im_res, shape, pad_idx, crop_idx =
preprocess(path_image=path_images[i],
File "/bif/software/FREESURFER/freesurfer-8.0.0/python/scripts/mri_synthseg",
line 577, in preprocess
im, _, aff, n_dims, n_channels, h, im_res = get_volume_info(path_image,
True)
File "/bif/software/FREESURFER/freesurfer-8.0.0/python/scripts/mri_synthseg",
line 1527, in get_volume_info
data_res = np.array(header['pixdim'][1:n_dims + 1])
File
"/bif/software/FREESURFER/freesurfer-8.0.0/python/lib/python3.8/site-packages/nibabel/wrapstruct.py",
line 310, in __getitem__
return self._structarr[item]
ValueError: no field of name pixdim
resuming program execution
ERROR: some problems occured for the following inputs (see corresponding errors
above):
/bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig.mgz
@#@FSTIME 2025:03:05:15:19:44 mri_synthseg N 11 e 8.65 S 0.72 U 4.20 P 56% M
575560 F 0 R 117516 W 0 c 260 w 14864 I 0 O 96 L 1.98 0.98 0.55
@#@FSLOADPOST 2025:03:05:15:19:53 mri_synthseg N 11 1.99 1.02 0.57
Linux synapse6 3.10.0-1062.12.1.el7.x86_64 #1 SMP Tue Feb 4 23:02:59 UTC 2020
x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub-AH002_ses-01_T1w.nii exited with ERRORS at Wed Mar 5 15:19:53
CET 2025
With the command "fslhd" I get the following for the file:
pixdim0 1.000000
pixdim1 1.000000
pixdim2 1.000000
pixdim3 1.000000
pixdim4 2.530000
pixdim5 0.000000
pixdim6 0.000000
pixdim7 0.000000
1) FreeSurfer version: 8.0.0
(freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a)
2) Platform: CentOS Linux release 7.7.1908
3) uname -a: Linux synapse6 3.10.0-1062.12.1.el7.x86_64 #1 SMP Tue Feb 4
23:02:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
4) recon-all.log: see attached
Thank you in advance. Best regards,
Andreas Lubig
Wed Mar 5 15:18:57 CET 2025
cd /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii
setenv SUBJECTS_DIR /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8
/bif/software/FREESURFER/freesurfer-8.0.0/bin/recon-all -s sub-AH002_ses-01_T1w.nii -i /bif/projects/migban/bidsdata/sub-AH002/ses-01/anat/sub-AH002_ses-01_T1w.nii.gz -all
subjid sub-AH002_ses-01_T1w.nii
setenv SUBJECTS_DIR /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8
FREESURFER_HOME /bif/software/FREESURFER/freesurfer-8.0.0
Actual FREESURFER_HOME /bif/software/FREESURFER/freesurfer-8.0.0
build-stamp.txt: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a
Linux synapse6 3.10.0-1062.12.1.el7.x86_64 #1 SMP Tue Feb 4 23:02:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize unlimited
coredumpsize 0 kbytes
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 64 kbytes
maxproc 4096
maxlocks unlimited
maxsignal 256366
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 62G 2.8G 42G 127M 17G 59G
Swap: 11G 0B 11G
########################################
program versions used
8.0.0 (freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a)
8.0.0
ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
8.0.0
ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
8.0.0
ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
mris_convert -all-info
ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:57-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
mri_motion_correct.fsl 8.0.0
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 8.0.0 TimeStamp: 2025/03/05-14:18:58-GMT BuildTime: Feb 3 2025 18:33:39 BuildStamp: freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a User: alubig Machine: synapse6 Platform: Linux PlatformVersion: 3.10.0-1062.12.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5
#######################################
GCADIR /bif/software/FREESURFER/freesurfer-8.0.0/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 /bif/software/FREESURFER/freesurfer-8.0.0/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
#######################################
/bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii
mri_convert /bif/storage/storage1/projects/migban/bidsdata/sub-AH002/ses-01/anat/sub-AH002_ses-01_T1w.nii.gz /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig/001.mgz
mri_convert /bif/storage/storage1/projects/migban/bidsdata/sub-AH002/ses-01/anat/sub-AH002_ses-01_T1w.nii.gz /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig/001.mgz
INFO: using NIfTI-1 sform (sform_code=1)
reading from /bif/storage/storage1/projects/migban/bidsdata/sub-AH002/ses-01/anat/sub-AH002_ses-01_T1w.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.998713, 0.042352, -0.027917)
j_ras = (-0.0431906, 0.998612, -0.0301534)
k_ras = (0.0266012, 0.0313203, 0.999155)
writing to /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig/001.mgz...
@#@FSTIME 2025:03:05:15:18:58 mri_convert N 2 e 3.14 S 0.01 U 2.95 P 94% M 48644 F 0 R 1561 W 0 c 13 w 392 I 0 O 19752 L 1.87 0.80 0.48
@#@FSLOADPOST 2025:03:05:15:19:01 mri_convert N 2 1.88 0.82 0.48
#--------------------------------------------
#@# MotionCor Wed Mar 5 15:19:02 CET 2025
Found 1 runs
/bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
Only one run found so motion
correction will not be performed. I'll
copy the run to rawavg and continue.
cp /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig/001.mgz /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/rawavg.mgz
mri_info /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/rawavg.mgz
rawavg.mgz ========================================
Volume information for /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/rawavg.mgz
type: MGH
intent: MRI (0)
dimensions: 176 x 256 x 256
voxel sizes: 1.000000, 1.000000, 1.000000
type: FLOAT (3)
fov: 256.000
dof: 1
xstart: -88.0, xend: 88.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 2530.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
nframes: 1
PhEncDir: UNKNOWN
FieldStrength: 0.000000
ras xform present
xform info: x_r = 0.9987, y_r = -0.0432, z_r = 0.0266, c_r = -0.2881
: x_a = 0.0424, y_a = 0.9986, z_a = 0.0313, c_a = -0.1328
: x_s = -0.0279, y_s = -0.0302, z_s = 0.9992, c_s = 10.3591
talairach xfm :
Orientation : RAS
Primary Slice Direction: axial
voxel to ras transform:
0.9987 -0.0432 0.0266 -86.0514
0.0424 0.9986 0.0313 -135.6911
-0.0279 -0.0302 0.9992 -111.2165
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 1
ras to voxel transform:
0.9987 0.0424 -0.0279 88.5825
-0.0432 0.9986 -0.0302 128.4325
0.0266 0.0313 0.9992 117.6615
0.0000 0.0000 0.0000 1.0000
/bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii
mri_convert /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/rawavg.mgz /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig.mgz --conform
mri_convert /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/rawavg.mgz /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig.mgz --conform
reading from /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/rawavg.mgz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.998713, 0.042352, -0.027917)
j_ras = (-0.0431906, 0.998612, -0.0301534)
k_ras = (0.0266012, 0.0313203, 0.999155)
volume geometry:
valid : -85139672
extent : (256, 256, 256)
voxel : ( 1.0000, 1.0000, 1.0000)
x_(ras) : (-1.0000, 0.0000, 0.0000)
y_(ras) : ( 0.0000, 0.0000, -1.0000)
z_(ras) : ( 0.0000, 1.0000, 0.0000)
c_(ras) : (-0.2881, -0.1328, 10.3591)
shears : ( 0.0000, 0.0000, 0.0000)
file : /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/rawavg.mgz
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 0 774 1000, flo=0, fhi=0.999, dest_type=0
Reslicing using trilinear interpolation
writing to /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig.mgz...
@#@FSTIME 2025:03:05:15:19:05 mri_convert N 3 e 3.89 S 0.01 U 3.76 P 97% M 60088 F 0 R 3496 W 0 c 12 w 244 I 0 O 9600 L 1.88 0.82 0.48
@#@FSLOADPOST 2025:03:05:15:19:09 mri_convert N 3 1.97 0.86 0.50
mri_add_xform_to_header -c /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/transforms/talairach.xfm /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig.mgz /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig.mgz
INFO: extension is mgz
@#@FSTIME 2025:03:05:15:19:09 mri_add_xform_to_header N 4 e 1.56 S 0.00 U 1.45 P 92% M 19548 F 0 R 1416 W 0 c 13 w 222 I 0 O 9600 L 1.97 0.86 0.50
@#@FSLOADPOST 2025:03:05:15:19:11 mri_add_xform_to_header N 4 1.97 0.87 0.51
mri_info /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig.mgz
orig.mgz ========================================
Volume information for /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig.mgz
type: MGH
intent: MRI (0)
dimensions: 256 x 256 x 256
voxel sizes: 1.000000, 1.000000, 1.000000
type: UCHAR (0)
fov: 256.000
dof: 1
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 2530.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
nframes: 1
PhEncDir: UNKNOWN
FieldStrength: 0.000000
ras xform present
xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -0.2881
: x_a = -0.0000, y_a = -0.0000, z_a = 1.0000, c_a = -0.1328
: x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 10.3590
talairach xfm : /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/transforms/talairach.xfm
Orientation : LIA
Primary Slice Direction: coronal
voxel to ras transform:
-1.0000 0.0000 0.0000 127.7119
-0.0000 -0.0000 1.0000 -128.1328
0.0000 -1.0000 0.0000 138.3590
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform:
-1.0000 0.0000 -0.0000 127.7119
-0.0000 0.0000 -1.0000 138.3590
-0.0000 1.0000 -0.0000 128.1328
-0.0000 -0.0000 -0.0000 1.0000
lta_convert --inlta identity.nofile --src /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/rawavg.mgz --trg /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig.mgz --outlta /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/rawavg2orig.lta
8.0.0
--inlta: identity.nofile input LTA transform.
--src: /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/rawavg.mgz src image (geometry).
--trg: /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig.mgz trg image (geometry).
--outlta: /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/rawavg2orig.lta output LTA.
LTA read, type : 1
1.00000 0.00000 0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000;
0.00000 0.00000 1.00000 0.00000;
0.00000 0.00000 0.00000 1.00000;
Writing LTA to file /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/rawavg2orig.lta...
lta_convert successful.
@#@FSTIME 2025:03:05:15:19:11 lta_convert N 8 e 0.21 S 0.00 U 0.20 P 98% M 2204 F 0 R 646 W 0 c 2 w 9 I 0 O 8 L 1.97 0.87 0.51
@#@FSLOADPOST 2025:03:05:15:19:11 lta_convert N 8 1.97 0.87 0.51
mri_synthstrip --threads 1 -i /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig.mgz -o /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/synthstrip.mgz
Configuring model on the CPU
Running SynthStrip model version 1
Input image read from: /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig.mgz
Processing frame (of 1): 1 done
Masked image saved to: /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/synthstrip.mgz
If you use SynthStrip in your analysis, please cite:
----------------------------------------------------
SynthStrip: Skull-Stripping for Any Brain Image
A Hoopes, JS Mora, AV Dalca, B Fischl, M Hoffmann
NeuroImage 206 (2022), 119474
https://doi.org/10.1016/j.neuroimage.2022.119474
Website: https://synthstrip.io
@#@FSTIME 2025:03:05:15:19:11 mri_synthstrip N 6 e 33.27 S 2.16 U 28.71 P 92% M 5860760 F 0 R 122244 W 0 c 345 w 7658 I 0 O 2440 L 1.97 0.87 0.51
@#@FSLOADPOST 2025:03:05:15:19:44 mri_synthstrip N 6 1.98 0.98 0.55
mri_synthseg --i /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig.mgz --o /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/synthseg.rca.mgz --threads 1 --vol /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/stats/synthseg.vol.csv --keepgeom --addctab --cpu
SynthSeg 2.0
using CPU, hiding all CUDA_VISIBLE_DEVICES
using 1 thread
addctab True
predicting 1/1
the following problem occurred with image /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig.mgz :
Traceback (most recent call last):
File "/bif/software/FREESURFER/freesurfer-8.0.0/python/scripts/mri_synthseg", line 324, in predict
image, aff, h, im_res, shape, pad_idx, crop_idx = preprocess(path_image=path_images[i],
File "/bif/software/FREESURFER/freesurfer-8.0.0/python/scripts/mri_synthseg", line 577, in preprocess
im, _, aff, n_dims, n_channels, h, im_res = get_volume_info(path_image, True)
File "/bif/software/FREESURFER/freesurfer-8.0.0/python/scripts/mri_synthseg", line 1527, in get_volume_info
data_res = np.array(header['pixdim'][1:n_dims + 1])
File "/bif/software/FREESURFER/freesurfer-8.0.0/python/lib/python3.8/site-packages/nibabel/wrapstruct.py", line 310, in __getitem__
return self._structarr[item]
ValueError: no field of name pixdim
resuming program execution
ERROR: some problems occured for the following inputs (see corresponding errors above):
/bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig.mgz
@#@FSTIME 2025:03:05:15:19:44 mri_synthseg N 11 e 8.65 S 0.72 U 4.20 P 56% M 575560 F 0 R 117516 W 0 c 260 w 14864 I 0 O 96 L 1.98 0.98 0.55
@#@FSLOADPOST 2025:03:05:15:19:53 mri_synthseg N 11 1.99 1.02 0.57
Linux synapse6 3.10.0-1062.12.1.el7.x86_64 #1 SMP Tue Feb 4 23:02:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub-AH002_ses-01_T1w.nii exited with ERRORS at Wed Mar 5 15:19:53 CET 2025
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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