External Email - Use Caution 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/1mn_DXGJRkbRZaR60gIIXGTJuR-LMjZIaTJCeez5OyFU1R7CR20ybjGOUz4tzd1AxyLGwPEti0x8dbFUB84ln0O_02-s6U0uTIK8MKNSC2PQi8YfCoEy1p0wItYQUPIb5iUXIN6xmG1NisixJAmoRH2aeiF1Hp2ua8Vwv7N3sV2qz3yq-FulWe5CIozSDdVtKxL-8HDqKu5m6Qmq6GfHUwkb68AW0vPu6pVuINPmzlucZN1FMBI-oVzetjru-RxRd8CEUnQYS0kfVzJqg3J8RkaraRyC-2GgBwrxi-VPObQTTobQn8Ty4Vssycv8t2gGm0EGMq-eSNszHNtFSMXl9qw/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/1VhsOWK6YuynPJZSTzGZep_xoqWFKijIbzVFTJkUW7wK3Iy1o63M730diiMYWK024Swr3mw9BBOIoTghZHgsLX-zhfP6VJWPQXHIZMmwb38t5iynLb8UTlDh2ES7braGKK28KbwDzrtuKHr6KKC__ikcHay2_nyeyuJS4IwgMAiqy9kk1c_jRMvKIvmNtHZnGGZHc2CGMi8aPtk5G4xQDteY56lAA64yYnRe_Lps-504c6Cz_3e4Nn8HCIblzADgs-Wd5j6sMe98DjAVApWr795qdo3M4CC3109D_5-l10o8bPlPWv6GeKT8TnmDAKUfThVbrpLKOB8jq9QJ6Pm1jmQ/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/1ErCkj9oNHbp_bA7yCLdfBWvX7scb1cY07IHh6AQwlr0Q3zCJ4IcHFkxbZr9N9-Fb3p_7f_Rj7fgU9VjWgvy2cYrVcVPY9I8bfHgnp_s07bPJZYfTWcnSF676gbZYnJ-f2K5HG5YZKutyFVDEwBpJIISXU6AF1SBCagt_FGxo2MUWESk7E1G5MUHxpJ8cIZraohAjo1bVt5Op9d7gogkHbEuKPr7ptaRm8u3Nd4cKu0sqeDH-mg6TeC4ouHRchhHjbyS1Jm1Q_H5phFu7QzCFmOA9oYVzyWulELZhSi1cXhutGdCqVx-4oaZoG4dsDb2gCW6Vk7SWImwBTop99lX4yg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > >
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