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Thank you so much, it worked!

Andreas

________________________________ Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu im Auftrag von Huang, Yujing YHUANG43@MGH.HARVARD.EDU Gesendet: Mittwoch, 5. März 2025 16:11:21 An: Freesurfer support list Betreff: Re: [Freesurfer] Freesurfer 8 - ValueError: no field of name pixdim

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

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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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> im Auftrag von Lubig, Andreas <andreas.lubig@rwth-aachen.demailto:andreas.lubig@rwth-aachen.de> Gesendet: Mittwoch, 5. März 2025 15:51:10 An: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] Freesurfer 8 - ValueError: no field of name pixdim

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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