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 (LCNhttps://www.nmr.mgh.harvard.edu/lab/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