I see ‘subjid sub-AH002_ses-01_T1w.nii’ in your attached recon-all.log. I think mri_synthseg is confused about the ‘.nii’ in your subjid. Can you change it to “_nii” and try again?
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu>
On Behalf Of Lubig, Andreas
Sent: Wednesday, March 5, 2025 10:06 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer 8 - ValueError: no field of name pixdim
External Email - Use Caution
Additional info:
The "fslhd" info I provided you in the last email was based on the original input file.
Thank you,
Andreas Lubig
Von:
freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> im Auftrag von Lubig, Andreas <andreas.lubig@rwth-aachen.de>
Gesendet: Mittwoch, 5. März 2025 15:51:10
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] Freesurfer 8 - ValueError: no field of name pixdim
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