Dear all,
We have recently fixed two problems in the subfield modules using the Matlab runtime:
1. We have moved on from MatlabR2014b to MatlabR2019b, which enables users to run the code in more modern versions of Mac OS.
2. A bug in the the longitudinal hippocampal subfield (& amygdala) segmentation was fixed, where the volumes reported in the text files did NOT account for linear deformations across timepoints, thus greatly underestimating change (I would *really* like to apologize for this).
Kind regards,
Juan Eugenio Iglesias http://www.jeiglesias.com
PS: these changes have happened in the development version, and will be incorporated into the next release.
Juan Eugenio Iglesias http://www.jeiglesias.com
On Apr 8, 2022, at 11:25, Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
Dear all,
We have recently fixed two problems in the subfield modules using the Matlab runtime:
1. We have moved on from MatlabR2014b to MatlabR2019b, which enables users to run the code in more modern versions of Mac OS.
2. A bug in the the longitudinal hippocampal subfield (& amygdala) segmentation was fixed, where the volumes reported in the text files did NOT account for linear deformations across timepoints, thus greatly underestimating change (I would *really* like to apologize for this).
Kind regards,
Juan Eugenio Iglesias http://www.jeiglesias.comhttp://www.jeiglesias.com/
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dear J.E.Iglesias,
can you please clarify me if this afects _longitudinal hippocampal subfield (& amygdala) segmentation_ in FREESURFER 7.1 version?
Thank you for reporting this issue.
with kind regards,
Yes, it does. Again: I’m terribly sorry about this. The reason why it slipped is that the segmentations themselves are fine, but the volumes in the text files are not.
The good news is that the bug leads to underestimated change, i.e., false negatives - rather than false positives.
Juan Eugenio Iglesias http://www.jeiglesias.com
On Apr 8, 2022, at 11:55, Otília C. d'Almeida <oalmeida@fmed.uc.ptmailto:oalmeida@fmed.uc.pt> wrote:
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dear J.E.Iglesias,
can you please clarify me if this afects longitudinal hippocampal subfield (& amygdala) segmentation in FreeSurfer 7.1 version?
Thank you for reporting this issue.
with kind regards,
-- Otília C.d'Almeida
A 2022-04-08 16:42, Iglesias Gonzalez, Juan E. escreveu:
PS: these changes have happened in the development version, and will be incorporated into the next release.
Juan Eugenio Iglesias MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.jeiglesias.comhttp://secure-web.cisco.com/12UgaNETRBDIuhmEYEAG3hSq_wMmIEvrS1NBJe2vO_MUV-UBHyivGBETPch6pwCI46j5l6MaJPaTBOsKGquDTacjZ7s2cjIU0rP8g99HF5EeyRHK3xVGqCp6t0HiR2R_BzyXCxXK0LhG-XdiiqrvL6kyY5sbX2yScmDxMDM9cij2asUIEEmoboj9isnf6uOfKCGE3xp5pfIJAMG2-musXcjKnz1nEZkLx0bSDJRNIJ9Cct_eWcR8gYtNe4cPnzMxge-DpVFqxtB955h42CA14K3yeOGjhakKVQ11bUbgEAfMjHjaHp7VJGCJpzde-30Y8/http%3A%2F%2Fwww.jeiglesias.com
On Apr 8, 2022, at 11:25, Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu> wrote: Dear all,
We have recently fixed two problems in the subfield modules using the Matlab runtime:
1. We have moved on from MatlabR2014b to MatlabR2019b, which enables users to run the code in more modern versions of Mac OS.
2. A bug in the the longitudinal hippocampal subfield (& amygdala) segmentation was fixed, where the volumes reported in the text files did NOT account for linear deformations across timepoints, thus greatly underestimating change (I would *really* like to apologize for this).
Kind regards,
Juan Eugenio Iglesias MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.jeiglesias.comhttp://secure-web.cisco.com/1iHj-ogL2KTV3-xiq6lKK_dSwjP5qTaZM_SXQ54jzwYt4bERaaLfdwdQ_m3nhP962VWzEsxg-p_aam4134_8ucgdM1U-zqldz51tTJf0Du2CxdFKdKDUucC_ILi_nGhw5PgR8YfyFdKrR_Kzr4pUWA2-mOe7yPmrYqXa4Kv9ZcWykzEdfj8s0G0Nid-H4vVAipi3SknUpHpfY6AUOEMk7Vfq5XyNPf4Vs7EVtXofDBrihgVONMZ_R9IGdSadNUmqYZq_XMx9RwzC8cJWvrCmKA6h8nb2cgWCrCmOP-KYUGf6qUJcb032SpOmj_fObkZRh/http%3A%2F%2Fwww.jeiglesias.com%2F
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/14hTdBOA_BoUA_3MvJqoR8Rhc8ncZPJbndy6D9vsjR60ALk36L4xJNALPbqdNTGK4WGhxghhKwSEaF2V_YovC8Sa3w3UiRnHBXLBvKO3PTwHvb32i2FTAqPb2CVS2pwQIapVodQc1Ld_h8b2cKjS6TfIGz0uR_B-YvEyCfl7hYL8lA_NDAK40rKzydldezdKfuS6ArKxf2FdAYmGMxealVn2CMJzfqXbk66Tao_6gs6iCkQic2AGg6tZmu7C4FFpWSn9tZOwkoTKK7OvoOisMMakpQI9ynpbR8N6ZI52lQbrwAF4giCOu0UMf83WWw_zv/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer 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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1VSdx4FrL3xfGDXv-NobJimgVSlbRhypBIpOK7PPDn4T1mxOqvYiXDB39POgug4H9JCKCoxqLHfEQTJXYPf5t9NGH4qSbV9azAYnXfIbjE9lQGbRHpCCzDv06Ze0YoY_5NM3yPl9ZiZF7YWWAfeqLuX94Q_gUvWZX6iycccnN8pp9gj7pCSAGGWJkaAAQZGs-eAfoBFpfxNDkpdCDD0av6egJHvK-7oHTzzISzH7Vt7y0jbsXkMF8i6Az4ErS9zVdskqX8kKzD0gpTnaDk2rlyucs2_kaStV_GV_OMoa2sRb9uydGflLOqYNoGkAuuh3D/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1VSdx4FrL3xfGDXv-NobJimgVSlbRhypBIpOK7PPDn4T1mxOqvYiXDB39POgug4H9JCKCoxqLHfEQTJXYPf5t9NGH4qSbV9azAYnXfIbjE9lQGbRHpCCzDv06Ze0YoY_5NM3yPl9ZiZF7YWWAfeqLuX94Q_gUvWZX6iycccnN8pp9gj7pCSAGGWJkaAAQZGs-eAfoBFpfxNDkpdCDD0av6egJHvK-7oHTzzISzH7Vt7y0jbsXkMF8i6Az4ErS9zVdskqX8kKzD0gpTnaDk2rlyucs2_kaStV_GV_OMoa2sRb9uydGflLOqYNoGkAuuh3D/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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thank you for reporting this, Dr Iglesias,
I have a few questions, as I'm currently analyzing results from longitudinal hippocampal segmentation:
1- When is the next release, including these fixes, due? 2- Is the development version, or a beta version, already available for download?
Best regards,
Andrei Bieger PhD Candidate in Biochemistry UFRGS - Porto Alegre, Brazil
Em sex., 8 de abr. de 2022 às 12:43, Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ@mgh.harvard.edu> escreveu:
PS: these changes have happened in the development version, and will be incorporated into the next release.
Juan Eugenio Iglesias http://secure-web.cisco.com/1PDf6T2xSBHl1SMSV6tWYjMOHxrohaeNeVxIPTVn1HrC-0E2...
On Apr 8, 2022, at 11:25, Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
Dear all,
We have recently fixed two problems in the subfield modules using the Matlab runtime:
- We have moved on from MatlabR2014b to MatlabR2019b, which enables users
to run the code in more modern versions of Mac OS.
- A bug in the the longitudinal hippocampal subfield (& amygdala)
segmentation was fixed, where the volumes reported in the text files did NOT account for linear deformations across timepoints, thus greatly underestimating change (I would *really* like to apologize for this).
Kind regards,
Juan Eugenio Iglesias http://secure-web.cisco.com/1PDf6T2xSBHl1SMSV6tWYjMOHxrohaeNeVxIPTVn1HrC-0E2...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1D5Xh0Il0D_aWOqhsxVVpaa4SDfXtZQo2cenB1rfYVi3ciu... 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/14z0qNfsCSgvyfjOycKQvQfViq1XurUID751smaxonSm7By... < https://secure-web.cisco.com/14z0qNfsCSgvyfjOycKQvQfViq1XurUID751smaxonSm7By... . 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.
Dear Andrei,
I don’t think there’s a fixed date for the next release, but the development version can be downloaded from here: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/
Cheers,
/E
Juan Eugenio Iglesias http://www.jeiglesias.com
On Apr 8, 2022, at 12:04, Andrei Bieger <andreibieger@gmail.commailto:andreibieger@gmail.com> wrote:
External Email - Use Caution
Thank you for reporting this, Dr Iglesias,
I have a few questions, as I'm currently analyzing results from longitudinal hippocampal segmentation:
1- When is the next release, including these fixes, due? 2- Is the development version, or a beta version, already available for download?
Best regards,
Andrei Bieger PhD Candidate in Biochemistry UFRGS - Porto Alegre, Brazil
Em sex., 8 de abr. de 2022 às 12:43, Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu> escreveu: PS: these changes have happened in the development version, and will be incorporated into the next release.
Juan Eugenio Iglesias MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.jeiglesias.comhttp://secure-web.cisco.com/1PDf6T2xSBHl1SMSV6tWYjMOHxrohaeNeVxIPTVn1HrC-0E2znEVpkCSkoMPSebgrPGLqaf-l0WCXK7av_GlREgjKaongxe4CIeR-ypUc2coz9iCYWWYe5kDcHWybbHopudqVD-D8l6w7YWryL2NFA0w-FKpqIHOdUZcBbYV7NscqBOhpkhdpfNylrxcuP1PJbo7_LSRYmoHatYrUrHTlqW8Rhjb3wpg3yzgLrHa820VnAvkU9049yNXhzJcs-NHtvwCKEU_eclq2mDlZaPnuepHvckZ86fcKnFl3qCzMdypsmVHhcCqUIH4qrRr_iLo3/http%3A%2F%2Fwww.jeiglesias.com
On Apr 8, 2022, at 11:25, Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
Dear all,
We have recently fixed two problems in the subfield modules using the Matlab runtime:
1. We have moved on from MatlabR2014b to MatlabR2019b, which enables users to run the code in more modern versions of Mac OS.
2. A bug in the the longitudinal hippocampal subfield (& amygdala) segmentation was fixed, where the volumes reported in the text files did NOT account for linear deformations across timepoints, thus greatly underestimating change (I would *really* like to apologize for this).
Kind regards,
Juan Eugenio Iglesias MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.jeiglesias.comhttp://secure-web.cisco.com/1B0H_WR2_QCDgcD11Y9XkyV4igqZ8dpdzY5JTxPrhpYwrRJhj7ev8J1fmXTFICsMuhN_HdplANhJu4qIq8YxUJLBtBNTib-sVGnee3QwqlJ2hal8yCsvG9Sq3xDMZNlHC6cL0K1PWhwOr_OV_n343Z2NzCKHJh3Shl2PvrfYQ5JHJuuedbYBvqPaO05urp5r41GSYai3oYdUetzf2aIt2VRuOBRM60qQEg2fllCaf_8AJp_eIcglIUtINOgXEIQ9AOoHAOpCLNKiwtko-8udMJUd0Izv1X_zvW3tPQCTc_DGw7MilYeee1mkQ_S58Tp7M/http%3A%2F%2Fwww.jeiglesias.com%2F
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-- Andrei Bieger _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Dear Eugenio,
Thanks so much for your update. I downloaded MATLAB 2019b and carried out the symlink to MCRv84 in the freesurfer folder but unfortunately I get the same error as last time when I run the Hip segmentation command. Is there something I need to differently? The error still tells me to download the 2014b compiler.
Best, Ashwati
-- Ashwati Vipin (PhD) Research Fellow - Dementia Research Centre Lee Kong Chian School of Medicine Nanyang Technological University, Singapore [signature_1630514251]
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@MGH.HARVARD.EDU Date: Friday, 8 April 2022 at 11:27 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] [IMPORTANT MESSAGE] Subfields & MCR problems solved Dear all,
We have recently fixed two problems in the subfield modules using the Matlab runtime:
1. We have moved on from MatlabR2014b to MatlabR2019b, which enables users to run the code in more modern versions of Mac OS.
2. A bug in the the longitudinal hippocampal subfield (& amygdala) segmentation was fixed, where the volumes reported in the text files did NOT account for linear deformations across timepoints, thus greatly underestimating change (I would *really* like to apologize for this).
Kind regards,
Juan Eugenio Iglesias http://secure-web.cisco.com/1PTK7JuvNl6hgLrwTpofMmNmebanWHzumoGfhsQvzlHrf_s9...
________________________________
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Andrei Bieger -
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Iglesias Gonzalez, Juan E. -
Otília C. d'Almeida