If you did not build FreeSurfer from the git repo, could you send the build stamp? It is located in a file called 'build-stamp.txt' in the FREESURFER_HOME directory.
Best, Jackson ________________________________ From: Nolan, Jackson <jnol...@mgh.harvard.edu> Sent: Monday, August 29, 2022 4:25 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; mdalaminba...@gmail.com <mdalaminba...@gmail.com> Subject: Re: [Freesurfer] segment_subregions failed Greetings, I am having some trouble reproducing that error. Could you send me the commit number of the git reop you cloned? Jackson Nolan, BSc - Programmer Laboratory for Computational Neuroimaging (LCN<https://www.nmr.mgh.harvard.edu/lab/lcn>) Athinoula A. Martinos Center for Biomedical Imaging Department of Radiology, Mass General Hospital (413) 244-8583 | jnol...@mgh.harvard.edu ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Md. Mamun Al-Amin <mdalaminba...@gmail.com> Sent: Monday, August 15, 2022 12:12 PM To: Freesurfer support list <Freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] segment_subregions failed External Email - Use Caution Hi Freesurfer experts, I have been trying to segment thalamus using segment_subregions command available in freesurfer 7.3.2. Unfortunately, I have been encountering the following error. IN-NSCC-050385:~ mdalamin$ segment_subregions thalamus --cross sub-0023 Step 1: preprocessing inputs for thalamus segmentation Running command: mri_convert /var/folders/3b/zd9p0z7s6nx_m1_xyg0tqqj0dgxn6r/T/tmpzh3k0uay/tempImage.mgz /var/folders/3b/zd9p0z7s6nx_m1_xyg0tqqj0dgxn6r/T/tmpzh3k0uay/tempImage.mgz -odt float -rt cubic -vs 0.5 0.5 0.5 Preprocessing took 6 seconds Step 2: aligning atlas to reference segmentation Traceback (most recent call last): File "/Applications/freesurfer/7.3.2//python/scripts/segment_subregions", line 99, in <module> subregions.run_cross_sectional(args.structure, parameters) File "/Applications/freesurfer/7.3.2/python/packages/freesurfer/subregions/process.py", line 52, in run_cross_sectional model.align_atlas_to_seg() File "/Applications/freesurfer/7.3.2/python/packages/freesurfer/subregions/core.py", line 240, in align_atlas_to_seg mask = mask.resize(1, interp='nearest') TypeError: resize() got an unexpected keyword argument 'interp' Any suggestions to troubleshoot this problem? Kind regards Md. Mamun Al-Amin, PhD --------------------------- Postdoctoral Fellow Stark Neuroscience Research Institute Indiana University School of Medicine 320 W. 15th Street, NB Bldg Rm 103 Indianapolis, IN 46202
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