I am also attaching the new core.py with the bug fix. You can unzip and copy it to $FREESURFER/python/gems/subregions

Best, Avnish ________________________________ From: Kumar, Avnish Avnish.Kumar@MGH.HARVARD.EDU Sent: Friday, September 23, 2022 11:47 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Cc: Nolan, Jackson JNOLAN5@mgh.harvard.edu; mdalaminbadal@gmail.com mdalaminbadal@gmail.com Subject: Re: [Freesurfer] segment_subregions failed

Hi Markus,

This bug has been fixedhttps://github.com/freesurfer/freesurfer/commit/9af3deaaf8aa44500b8ccf136179afe8c003a172 in the dev branch of Freesurfer (FS). You can get the changes in your local copy of FS by either git checkout the python/gems/subregions/core.py file into the appropriate subfolder (<FS_install_dir>/python/gems/subregions) where you installed FS or you could simply edit the core.py file at that location as in the bug fixhttps://github.com/freesurfer/freesurfer/commit/9af3deaaf8aa44500b8ccf136179afe8c003a172.

Best, Avnish ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Markus Handal Sneve m.h.sneve@psykologi.uio.no Sent: Wednesday, September 21, 2022 2:35 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Cc: Nolan, Jackson JNOLAN5@mgh.harvard.edu; mdalaminbadal@gmail.com mdalaminbadal@gmail.com Subject: Re: [Freesurfer] segment_subregions failed

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Hi,

Sorry if this ends up in the wrong place, had to reactivate my FS-mailing list account.

So I get the exact same error as reported by Mamun Al-Amin when running segment_subregion (FS v7.3.2).

Fresh terminal, no other FS version running in the background, build-stamp.txt shows the correct version.

Hopefully you can see the screenshot below, sadly cannot ctrl-c text out of our cluster

[cid:02AE0EFB-80BC-4895-B44D-AC05CB77D890]

Thanks!

Markus Handal Sneve, Ph.D. Center for Lifespan Changes in Brain and Cognition Department of Psychology University of Oslo

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Hi again,

I noted one thing when applying the fix: the python package “gems” is not included in the latest Freesurfer release (7.3.2). The relevant core.py still seems to reside in the old structure, i.e. in $FREESURFER/python/packages/freesurfer/subregions

The new core.py imports from “gems” so copy-pasting the file probably won’t work in 7.3.2. However, applying the bug fix (“interp”—>”nearest”) locally solves the issue.

[cid:77CED678-7E6B-4191-A81E-7939CCDD3DF5]

Thanks! Markus

On 26 Sep 2022, at 14:16, Markus Handal Sneve <m.h.sneve@psykologi.uio.nomailto:m.h.sneve@psykologi.uio.no> wrote:

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Thanks a lot! - Markus

On 26 Sep 2022, at 13:27, Kumar, Avnish <Avnish.Kumar@MGH.HARVARD.EDUmailto:Avnish.Kumar@MGH.HARVARD.EDU> wrote:

I am also attaching the new core.py with the bug fix. You can unzip and copy it to $FREESURFER/python/gems/subregions

Best, Avnish ________________________________ From: Kumar, Avnish <Avnish.Kumar@MGH.HARVARD.EDUmailto:Avnish.Kumar@MGH.HARVARD.EDU> Sent: Friday, September 23, 2022 11:47 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Nolan, Jackson <JNOLAN5@mgh.harvard.edumailto:JNOLAN5@mgh.harvard.edu>; mdalaminbadal@gmail.commailto:mdalaminbadal@gmail.com <mdalaminbadal@gmail.commailto:mdalaminbadal@gmail.com> Subject: Re: [Freesurfer] segment_subregions failed

Hi Markus,

This bug has been fixedhttps://secure-web.cisco.com/1ZL45XR-5UsWffUupkhF5mP1lE9Wte3gMYZIAvcv5z-sYTM0U579d0CfH4JJw2N_DI_ydEF35mno9mCFCdBEgrw_M0qRpDu5ahWNGkwDXPRuU_3V-NI3vFeg5qaKkVkkXJ9_abs7fLDGRtgyGIRYbRk1pFxNjF1Toa_CxRC0-S-wTChIpM7FtzABA1JhD1l6ldMqln1hluQ9o5iG4x8BiEu4eIo_ZeSFdRj1hKykOUalDiLnB_R0Z_9RcW9aVetZxeWyQwEF5jQQMo9ra5VQAwy_Pp3KHo19qr3gdJmAI8xBEo0xoj_RgVeY1svxNaph3yb8QosszP7oCyl8Agb3O__J8iyfBbGVgbdW8_jahfqg/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fcommit%2F9af3deaaf8aa44500b8ccf136179afe8c003a172 in the dev branch of Freesurfer (FS). You can get the changes in your local copy of FS by either git checkout the python/gems/subregions/core.py file into the appropriate subfolder (<FS_install_dir>/python/gems/subregions) where you installed FS or you could simply edit the core.py file at that location as in the bug fixhttps://secure-web.cisco.com/1ZL45XR-5UsWffUupkhF5mP1lE9Wte3gMYZIAvcv5z-sYTM0U579d0CfH4JJw2N_DI_ydEF35mno9mCFCdBEgrw_M0qRpDu5ahWNGkwDXPRuU_3V-NI3vFeg5qaKkVkkXJ9_abs7fLDGRtgyGIRYbRk1pFxNjF1Toa_CxRC0-S-wTChIpM7FtzABA1JhD1l6ldMqln1hluQ9o5iG4x8BiEu4eIo_ZeSFdRj1hKykOUalDiLnB_R0Z_9RcW9aVetZxeWyQwEF5jQQMo9ra5VQAwy_Pp3KHo19qr3gdJmAI8xBEo0xoj_RgVeY1svxNaph3yb8QosszP7oCyl8Agb3O__J8iyfBbGVgbdW8_jahfqg/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fcommit%2F9af3deaaf8aa44500b8ccf136179afe8c003a172.

Best, Avnish ________________________________ 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 Markus Handal Sneve <m.h.sneve@psykologi.uio.nomailto:m.h.sneve@psykologi.uio.no> Sent: Wednesday, September 21, 2022 2:35 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Nolan, Jackson <JNOLAN5@mgh.harvard.edumailto:JNOLAN5@mgh.harvard.edu>; mdalaminbadal@gmail.commailto:mdalaminbadal@gmail.com <mdalaminbadal@gmail.commailto:mdalaminbadal@gmail.com> Subject: Re: [Freesurfer] segment_subregions failed

External Email - Use Caution

Hi,

Sorry if this ends up in the wrong place, had to reactivate my FS-mailing list account.

So I get the exact same error as reported by Mamun Al-Amin when running segment_subregion (FS v7.3.2).

Fresh terminal, no other FS version running in the background, build-stamp.txt shows the correct version.

Hopefully you can see the screenshot below, sadly cannot ctrl-c text out of our cluster

<PastedGraphic-1.png>

Thanks!

Markus Handal Sneve, Ph.D. Center for Lifespan Changes in Brain and Cognition Department of Psychology University of Oslo

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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1kV2gS9qQ2lauKFaezE5un5MziPCroMwRqsvUWSMP885UMn... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1MNjwZb8JO7suV6YOniAdhiqNSTdRtiDaZWN8J_T_ONMbFq... https://secure-web.cisco.com/1MNjwZb8JO7suV6YOniAdhiqNSTdRtiDaZWN8J_T_ONMbFq7jYEQ31_ShOuxmadsey1AkiggOW1zbRao979b-aaXlUIkxS8J8_20vLfVvbu4SXZIOgv8aBZKzBiDawCiPY2dY7LE0Jcgo_V6dNh0gjCp8EJSySKH0_RbcQJDeAI5HfHLQ3KqKbPXdhM6b5c4TJpe9LkAw5fVElFzngUMOeacWU53eQmhfW6t92hQHLlpJfmVvIRSwiY4HOP1onVIV7hNwWzO8oIIhKlwqrfUdc0rhiuioMsCiCLsqZWEZRQkLcNACKHkXA-ekPD9DFM7nnbxKBtMKulgFgQ-rKMOOu3-CkHmIyo7gi2T36tJooF4/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.