External Email - Use Caution
Dear Freesurfer community,
I am using the freesurfer version through a singularity container (https://secure-web.cisco.com/1j_Zv2QItcuWtdQRfU3BocTH20Tz0V5FYnvMZKQNUHVHrSJ...) in a HPC cluster. It all ent well until I extracted the subcortical regions, where I see that for all of my subjects the values of Thalamus-proper are 0. When I look further into it, I see that my FreeSurferColorLUT.txt file only includes Thalamus but not Thalamus-proper.
I found this thread which mentions that the thalamus-proper was removed from recent FreeSurfer versions: https://secure-web.cisco.com/1_BT-tajm4M7yDBVb5BfWwjdB0iHk_Liz1vM5WOL3zLziLY...
Unfortunately, when I try to look for information online on whether they are exactly the same or whether they differ, I only found the FreeSurfer wiki page about the FreeSurferColorLUThttps://secure-web.cisco.com/1i1A_DRuhjTo1dIQFd0ggAD58K_mWkVlkDzs4I3ydFj4x2PSfJKlkECGW1m_jl_3SnVkM2VK8gX013hhQvpb8AToOScZftM9Yi8cVea02oLmG82k-IT0ifY-m5uR6JmGJKbfzMC0kUoCXsNxK1sqB9JZlmIkOsVNzosZOsxATx6EKMCQwSEuWEKJN151ZoV0MGTcdSjb5gc0Hb0aJtyWpvpfExcYSFLcZwzJLD7VDTHVvkojpnicN0yj1TYrR9GLBl-MKjuixCNBSSmJb4cVAMA/https%3A%2F%2Fsmex12-5-en-ctp.trendmicro.com%2Fwis%2Fclicktime%2Fv1%2Fquery%3Furl%3Dhttps%253a%252f%252ffreesurfer.net%252ffswiki%252fFsTutorial%252fAnatomicalROI%252fFreeSurferColorLUT%26umid%3D4f7a637e-67b0-4416-a892-6e83d48df433%26auth%3D42a667e5a39731575079a1e93e003e107f6f6070-4399b04978da4baacaa8b291e6dbcba23c36bac3(i.e., look up table) which includes this note: “* Thalamus-Proper is the correct segmentation for the Thalamus.” But this is a page from 2015 so might not be up to date anymore. In this threadhttps://secure-web.cisco.com/1IMfKsWyLM9gWH6vW81VZUrGlkiDnwKUtLgzVagH0ZHERnJcjgD_orZ_hmtTZZQ9NnMrN6qutC7nkPGShfcsV59D3RRjiMCVG0XPExlQaCvuY0alOkE9reWtRZhryuqezTVxc2F1XOgrvpcV6U-mZPnSEDcFsvC12tqBVSt4wKIL8bFG73CPyhnkZtfByqC8q8ehZU3O5yZalgoUZfp1lXKX5NKWHXProGRQ7a_UVEPYRzLrbC0EzfKgG7NebRddzwBrGr1EMHiy2Dcng-gF98Q/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg56219.html from 2017it was also discussed that the thalamus-proper is the correct one but it is also stated that name should be changed, so maybe they have done this now.
Basically - do I need to re-run the recon-all with a different freesurfer version to extract Thalamus-proper or has this been replaced by Thalamus now?
Thanks!!
A
It has been replaced by thalamus now
On 10/8/2021 6:56 AM, Cubillo, Ana wrote:
External Email - Use Caution
Dear Freesurfer community,
I am using the freesurfer version through a singularity container (*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://hub.docker.com/r/freesurfer/freesurfer https://secure-web.cisco.com/1j_Zv2QItcuWtdQRfU3BocTH20Tz0V5FYnvMZKQNUHVHrSJnEYT6SaYNXa25BmI-JbPTJCJ1GCrzzhmfuUc3ZZ6iK4JDuJS0kjv_hdt8Wl2-pAx2OFoyTnLpSWLjFHaNiCO3Auaa6dMpJAa1xy951xqo1OEVnAlu0RopFeH2w_MdBlz2ShK34SzMjt6QZgGKKT_j_wq90FX57ea3AeZLYVip_4puSVVm0SxH2lhd8d64M_nd6ntsB0KiwlcTMdl6dMVQrglmTwcHpNQ0zqkVVTw/https%3A%2F%2Fhub.docker.com%2Fr%2Ffreesurfer%2Ffreesurfer) in a HPC cluster. It all ent well until I extracted the subcortical regions, where I see that for all of my subjects the values of Thalamus-proper are 0. When I look further into it, I see that my FreeSurferColorLUT.txt file only includes Thalamus but not Thalamus-proper.
I found this thread which mentions that the thalamus-proper was removed from recent FreeSurfer versions: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://community.mrtrix.org/t/thalamus-proper-removed-from-freesurfercolorl... https://secure-web.cisco.com/1_BT-tajm4M7yDBVb5BfWwjdB0iHk_Liz1vM5WOL3zLziLYePvaK0uInTUY0xg9P5m3uiTYSaXoW_Fa5AkGtqpirqX5sQ2yuBrtVaTL2izRUOL9Qumey2i2SO8s7bnQ_z-C98X57FclQ5feF7aKJ7cCo_fnmIgADiyXp2U8LfMjI3iJYHIbuOpqOPsqVKV94Q2MYQ3zRUIAle0DYHwDDHrQznqf4agNjoHb8Z_Z26hMN0ou9Aq-X_EP9efCfJ35CQ-WhrCW2iaSPHwaotmWPxLg/https%3A%2F%2Fcommunity.mrtrix.org%2Ft%2Fthalamus-proper-removed-from-freesurfercolorlut-txt%2F3721%2F2 Unfortunately, when I try to look for information online on whether they are exactly the same or whether they differ, I only found the FreeSurfer wiki page about the FreeSurferColorLUT https://secure-web.cisco.com/1i1A_DRuhjTo1dIQFd0ggAD58K_mWkVlkDzs4I3ydFj4x2PSfJKlkECGW1m_jl_3SnVkM2VK8gX013hhQvpb8AToOScZftM9Yi8cVea02oLmG82k-IT0ifY-m5uR6JmGJKbfzMC0kUoCXsNxK1sqB9JZlmIkOsVNzosZOsxATx6EKMCQwSEuWEKJN151ZoV0MGTcdSjb5gc0Hb0aJtyWpvpfExcYSFLcZwzJLD7VDTHVvkojpnicN0yj1TYrR9GLBl-MKjuixCNBSSmJb4cVAMA/https%3A%2F%2Fsmex12-5-en-ctp.trendmicro.com%2Fwis%2Fclicktime%2Fv1%2Fquery%3Furl%3Dhttps%253a%252f%252ffreesurfer.net%252ffswiki%252fFsTutorial%252fAnatomicalROI%252fFreeSurferColorLUT%26umid%3D4f7a637e-67b0-4416-a892-6e83d48df433%26auth%3D42a667e5a39731575079a1e93e003e107f6f6070-4399b04978da4baacaa8b291e6dbcba23c36bac3(i.e., look up table) which includes this note: “* Thalamus-Proper is the correct segmentation for the Thalamus.” But this is a page from 2015 so might not be up to date anymore. In this thread https://secure-web.cisco.com/1IMfKsWyLM9gWH6vW81VZUrGlkiDnwKUtLgzVagH0ZHERnJcjgD_orZ_hmtTZZQ9NnMrN6qutC7nkPGShfcsV59D3RRjiMCVG0XPExlQaCvuY0alOkE9reWtRZhryuqezTVxc2F1XOgrvpcV6U-mZPnSEDcFsvC12tqBVSt4wKIL8bFG73CPyhnkZtfByqC8q8ehZU3O5yZalgoUZfp1lXKX5NKWHXProGRQ7a_UVEPYRzLrbC0EzfKgG7NebRddzwBrGr1EMHiy2Dcng-gF98Q/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg56219.html from 2017it was also discussed that the thalamus-proper is the correct one but it is also stated that nameshould be changed, so maybe they have done this now.
Basically - do I need to re-run the recon-all with a different freesurfer version to extract Thalamus-proper or has this been replaced by Thalamus now?
Thanks!!
A
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Cubillo, Ana -
Douglas N. Greve