External Email - Use Caution 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 <awo...@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/171ahSlRX4vDMQD6prCFbKOWLRaTb3TeYqaUPEw1RHNCsVe3tGhp2kLFzWK3DJBLSx-UgUbpykn2uadM_p35sDDmGGUu-97iv7xWk1uOF7fCA5zzinTnVGh-ThVdtMXCb9wrWbtVUluLHZqPDir9P61Y41lyQx6J8ExkHyMN3nDhsdJG3NKQ0YCbHpN6OXcbMXy6k6AGFamQP8CZo_1lxhCV5WCZD26w_wkehvkhvpWl7Dd8-79VHNEEopR-cjICmGSqmg7GHDHiBc1SkoGDf-Hrij5PrwTlD6yLqb5U83FrN3wzFoW9dq-kjChSC2PKLUxnb8MKiKmHqCpn6WhL36g/https%3A%2F%2Fhub.docker.com%2Fr%2Ffreesurfer%2Ffreesurfer%3A7.1.1) > and > I replaced the /usr/local/freesurfer with this version: > https://secure-web.cisco.com/1kTRkrixWgWU1iw8Qqe5X9q-Fz5Cs0dBxd03uelbVyK3aahbt-NDyUMFDpzSxsqPZKM2WUqoyOMnywfNkFMZP_5uzLcnYmhRlPJwt6eoOMbmo_-bFRvK9YV6H-tS6FGTlH7lZCDQw4Tr2_WlN4a-2ByEqPmRw_RHrKq8SU2Sk4aNDWHoS5lPwMqIs5td3Mpd2KWBbQCJ7f20xoIDdqxcxnMQ5K3m5nC2y5sS1QzfGMOTXHSLiC-7D-Dr218ggnoS6u3Eg-UqVFYGtZZm_ACvQ6OSAYJ7z7VdTRgX6PRuMv1mQLduPWJ1CXUv1RmUDCBI4mZKBJZd0GkBTpL_9yzF30w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2F > (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 <fsbu...@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 <awo...@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-grzSWGdWAjGnbbKEWKa1RY2Vnq_1XIzUp_Pw9JiPTv-9RURdKW8JxITiQ4fHQd52cDeNtKyxObaVNhoMm7eCG4MHWe-oNp1ZhUspCOTt4mUS8YvG-Sz5AQUHtIpiftry8PqNBXsiCnyqtBPZSx5sVUIhwiDZLnBUH-S8whGTknUkdvCCHrnJwXFuWYiYGfGjgQd4LNScX6tqKhbyUleuP2jj3nSP5hC-IReTKIYV44idgR-A487NfahyJKGCBF1HucAshKd93xsa1R3xEnhBVJyvfG0jZGi_K1xFoPWlrA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> >> >>
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