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Hi!

I've managed to debug the problem and it turns out that it was generated by the mri_convert function - it produced a corrupted native.mgz image that synthseg couldn't correctly read. I encounter this problem when pulling the freesurfer:7.4.1 from dockerhub and when I was using a version downloaded from the freesurfer website. Replacing the mri_convert script with a one from a previous release (7.1.1) solved the problem, but I'm just letting you know, in case that's a more general issue (and in all cases I was running the script in a singularity containers).

Best wishes, Agata

pon., 26 lut 2024 o 11:02 Agata Wolna awolna@mit.edu napisał(a):

Hi!

Thanks for getting back to me. I'm running it on CentOS Linux 7 in a singularity container. What I did is to pull the freesurfer container from the DockerHub (https://secure-web.cisco.com/171ahSlRX4vDMQD6prCFbKOWLRaTb3TeYqaUPEw1RHNCsVe...) and I replaced the /usr/local/freesurfer with this version: https://secure-web.cisco.com/1kTRkrixWgWU1iw8Qqe5X9q-Fz5Cs0dBxd03uelbVyK3aah... (build-stamp is freesurfer-linux-centos7_x86_64-dev-20240209-8d5b885).

Do you think that this might be an issue related to the differences in dependencies for the 7.1.1 and the dev version that I replaced the 7.1.1 with? Also, if you happen to have a containerized version of the newest dev version (or any version higher than 7.4, as I assume they would all support the recon-all-clinical function, right?) maybe I could just pull the entire container from somewhere and see if it solves the problem?

Best wishes, Agata

niedz., 25 lut 2024 o 21:56 fsbuild fsbuild@contbay.com napisał(a):

...

It could help to know what OS version and what Freesurfer version you are running. From your path /usr/local/freesurfer it looks like you are running a Freesurfer release, e.g.., 7.4.1.

• R.

On Feb 25, 2024, at 21:45, Agata Wolna awolna@mit.edu wrote:

    External Email - Use Caution

Hi!

I'm trying to run recon-all-clinical but I'm running into an error with the SynthSeg at the very beginning. Do you have any hints what the problem might be here? Here's the full error message:

the following problem occured with image [mypath]/mri/native..mgz : Traceback (most recent call last): File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 303, in predict image, aff, h, im_res, shape, pad_idx, crop_idx = preprocess(path_image=path_images[i], File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 554, in preprocess im, _, aff, n_dims, n_channels, h, im_res = get_volume_info(path_image, True) File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 1456, in get_volume_info im, aff, header = load_volume(path_volume, im_only=False) File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 1377, in load_volume x = nib.load(path_volume) File "/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/loadsave.py", line 110, in load img = image_klass.from_filename(filename, **kwargs) File "/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/dataobj_images.py", line 503, in from_filename return klass.from_file_map(file_map, mmap=mmap, keep_file_open=keep_file_open) File "/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/freesurfer/mghformat.py", line 526, in from_file_map header = klass.header_class.from_fileobj(mghf) File "/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/freesurfer/mghformat.py", line 171, in from_fileobj + int(klass._data_type_codes.bytespervox[tp]) * np.prod(hdr_str_to_np['dims']) KeyError: 10

resuming program execution

ERROR: some problems occured for the following inputs (see corresponding errors above): [mypath]/mri/native..mgz Error in SynthSeg

Best, Agata _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1eGi6jacCYjWFzgK78COanoaiX78kP8QzTk4XoggQitB-gr...