External Email - Use Caution
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