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 <JNOLAN5@mgh.harvard.edu>
Sent: Monday, August 29, 2022 4:25 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; mdalaminbadal@gmail.com <mdalaminbadal@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)
Athinoula A. Martinos Center for Biomedical Imaging
Department of Radiology, Mass General Hospital
(413) 244-8583 | jnolan5@mgh.harvard.edu
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Md. Mamun Al-Amin <mdalaminbadal@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