Thanks for the info about the build,

Yes, I think the issue is coming from some old information on your system, as that build stamp is from 2009. You may have both versions of FreeSurfer installed on your system, but the old version is taking priority.

If both are installed on your system, you can start with a fresh terminal, without sourcing FreeSurfer, then run the setup script for 7.3.2. Sourcing multiple versions in the same terminal session can cause issues finding the correct version of the utilities.

Otherwise, I would recommend removing the FreeSurfer files you currently have on your system and then doing a clean install of 7.3.2.

Best, Jackson ________________________________ From: Md. Mamun Al-Amin mdalaminbadal@gmail.com Sent: Wednesday, August 31, 2022 6:02 AM To: Nolan, Jackson JNOLAN5@mgh.harvard.edu Subject: Re: [Freesurfer] segment_subregions failed

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Hi Jackson, I do not know how freesurfer was built (from the git repo or somewhere else). I requested our HPC department at Indiana university to install an updated version of freesurfer. Interestingly, I see the 'build-stamp.txt' file contains only the text "freesurfer-x86_64-redhat-linux-gnu-dev4-20090216". Do you think this old information is responsible for this failure? 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

On Tue, Aug 30, 2022 at 12:53 PM Nolan, Jackson <JNOLAN5@mgh.harvard.edumailto:JNOLAN5@mgh.harvard.edu> wrote: 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.edumailto:JNOLAN5@mgh.harvard.edu> Sent: Monday, August 29, 2022 4:25 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>; mdalaminbadal@gmail.commailto:mdalaminbadal@gmail.com <mdalaminbadal@gmail.commailto: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://secure-web.cisco.com/1MlxQMEDBghD0Z_Lu-oEVCntF2aEel3BSjl7JHkL3B0wmx2x0wT6Hj2_D3n9kEH2vB7Pm0In2Gr-sQ4sMpQeIxmjM7fGlBPrY8verE9VGA_RgKBYtxBEOYUHWLSKiwEi7Pl_xkdkfGPL-khA4tGD75YCkq-wz-L3DaLTzJOZpN4vHUbk8HP-DTnh-dmI20bzM_Y7krCBS1FpS4-aezqqjE-YjFP_djmmN0iuQruWQafAmkZ7lDNf4R0uU991vCSoo8q3X7pIX-ekrjOw27BNIPi7TcBS15M0MebEaYhflZ9T_xj5FmjVL88ZyOeYEj0ol/https%3A%2F%2Fwww.nmr.mgh.harvard.edu%2Flab%2Flcn) Athinoula A. Martinos Center for Biomedical Imaging Department of Radiology, Mass General Hospital (413) 244-8583 | jnolan5@mgh.harvard.edumailto:jnolan5@mgh.harvard.edu ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Md. Mamun Al-Amin <mdalaminbadal@gmail.commailto:mdalaminbadal@gmail.com> Sent: Monday, August 15, 2022 12:12 PM To: Freesurfer support list <Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] segment_subregions failed

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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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