RE: [caret-users] Macaque Neuroanatomy
Hi David, Thanks so very much for your kind reply. I shall take a look at the CoCoMac database. Best wishes, Hamied From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David Vanessen Sent: 22 March 2007 23:36 To: Caret, SureFit, and SuMS software users Cc: Rolf Kötter Subject: Re: [caret-users] Macaque Neuroanatomy Hamied, The best source I know of for your questions is the CoCoMac database developed by Rolf Kotter and colleagues. http://cocomac.org/home.htm You have to get an account, but once you do, you can search for connections of any area of interest and then click on the area abbreviation to get a popup window showing the full name and reference. The results are: TA: Temporal area TA TE: Inferotemporal area TE PA#1: Postcentral area PA von Bonin, G; Bailey, P http://134.95.56.239/URLSearch.asp?OutputType=HTML_BrowserUser=vanessenPassword=v1v2v3Search=LiteratureSortBy=YearSortOrder=ASCDetails=Status,BrainSites,Methods,Relations,InjectionsSearchString=%28%27BB47%27%29+%5BLitID%5D 1947 The Neocortex of Macaca Mulatta IPa: Intraparietal sulcus associated area in the superior temporal sulcus TAa: Temporal area TAa Seltzer, B; Pandya, DN 1978 Site Ts1: Area temporalis superior 1 Galaburda, AM; Pandya, DN 1983 The intrinsic architectonic and connectional organization of the superior temporal region of the rhesus monkey Site NeuroNames in BrainInfo (http://braininfo.rprc.washington.edu/) is another useful source of terminology information but doesn't yet have full entries for the ones you asked about. David Van Essen On Mar 22, 2007, at 12:27 PM, Hamied Haroon wrote: Hello, I'm not a neuroanatomist, but I want to find the neuroanatomical names for the temporal areas in the F99UA1 macaque parcellated according to C:\Caret5\CARET_TUTORIAL_SEPT06\MACAQUE\Macaque.F99UA1.BOTH.LewisVE00+orig Most of the abbreviations given in the associated paint colour key are listed explicitly in the LVE00 reference paper (Lewis JW and Van Essen DC, J Comp Neurol, 428:112-37, 2000). Unfortunately the following abbreviations don't appear to be given in full in this reference paper or in the other references cited (Seltzer B and Pandya DN, Brain Res, 149:1-24, 1978, and Cusick CG et al., J Comp Neurol, 360:513-35, 1995): IPa PA TAa TE Ts I would be very grateful if anyone could please let me know what these abbreviations are in full. Many thanks in anticipation. Hamied Hamied Ahmad Haroon PhD AMInstP Research Associate in MR Neuroimaging Division of Imaging Science and Biomedical Engineering Faculty of Medical and Human Sciences The University of Manchester Room G.603 Stopford Building, Oxford Road, Manchester M13 9PT England, United Kingdom Tel: +44 (0)161 275 6871 Fax: +44 (0)161 275 5145 Email: [EMAIL PROTECTED] Web: www.isbe.man.ac.uk/~hharoon ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
RE: [caret-users] Macaque Neuroanatomy
Hi Rolf, Thanks very much for the information. I actually got a bit lost in CoCoMac when I first went in but now you've made it clear to me how the search is supposed to be used. Great! Hi Jonas, I would very much like to try out your BSTC for you. It sounds like you guys are doing some much-needed developments, especially for those of us who have to know neuroanatomy without having a background in the field. Many thanks. Best wishes, Hamied -Original Message- From: Rolf Kötter [mailto:[EMAIL PROTECTED] Sent: 23 March 2007 16:55 To: Hamied Haroon; Caret, SureFit,and SuMS software users Cc: JonasBarth Subject: Re: [caret-users] Macaque Neuroanatomy David, Hamied et al.: after login with CoCoMac you can obtain the full names even more easily by typing the individual acronym into the keyword box and then press any one of the three buttons (Connectivity, Mapping, Literature). For this purpose the Mapping relations statements would be the most informative. BTW: Recognizing the use of CoCoMac as a tool that keeps track of different neuroanatomical names my student Jonas Barth has started to develop a Brain Structure Terminology Converter (BSTC) which features an interface that finds structures with similar spatial, terminological and/or orthographic properties. If you like to try it then please ask him for access to it (I include him in the cc of this e-mail). We would very much like to get feedback from external users. Rolf Hamied Haroon wrote: Hi David, Thanks so very much for your kind reply. I shall take a look at the CoCoMac database. Best wishes, Hamied *From:* [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] *On Behalf Of *David Vanessen *Sent:* 22 March 2007 23:36 *To:* Caret, SureFit, and SuMS software users *Cc:* Rolf Kötter *Subject:* Re: [caret-users] Macaque Neuroanatomy Hamied, The best source I know of for your questions is the CoCoMac database developed by Rolf Kotter and colleagues. _http://cocomac.org/home.htm _ You have to get an account, but once you do, you can search for connections of any area of interest and then click on the area abbreviation to get a popup window showing the full name and reference. The results are: TA: Temporal area TA TE: Inferotemporal area TE PA#1: Postcentral area PA von Bonin, G; Bailey, P http://134.95.56.239/URLSearch.asp?OutputType=HTML_BrowserUser=vanessenPassword=v1v2v3Search=LiteratureSortBy=YearSortOrder=ASCDetails=Status,BrainSites,Methods,Relations,InjectionsSearchString=%28%27BB47%27%29+%5BLitID%5D 1947 The Neocortex of Macaca Mulatta IPa: Intraparietal sulcus associated area in the superior temporal sulcus TAa: Temporal area TAa _Seltzer, B; Pandya, DN _1978 Site Ts1: Area temporalis superior 1 _Galaburda, AM; Pandya, DN_ 1983 The intrinsic architectonic and connectional organization of the superior temporal region of the rhesus monkey Site NeuroNames in BrainInfo (http://braininfo.rprc.washington.edu/) is another useful source of terminology information but doesn't yet have full entries for the ones you asked about. David Van Essen On Mar 22, 2007, at 12:27 PM, Hamied Haroon wrote: Hello, I'm not a neuroanatomist, but I want to find the neuroanatomical names for the temporal areas in the F99UA1 macaque parcellated according to C:\Caret5\CARET_TUTORIAL_SEPT06\MACAQUE\Macaque.F99UA1.BOTH.LewisVE00+orig Most of the abbreviations given in the associated paint colour key are listed explicitly in the LVE00 reference paper (Lewis JW and Van Essen DC, /J Comp Neurol/, *428*:112-37, 2000). Unfortunately the following abbreviations don't appear to be given in full in this reference paper or in the other references cited (Seltzer B and Pandya DN, /Brain Res/, *149*:1-24, 1978, and Cusick CG et al., /J Comp Neurol/, *360*:513-35, 1995): IPa PA TAa TE Ts I would be very grateful if anyone could please let me know what these abbreviations are in full. Many thanks in anticipation. Hamied Hamied Ahmad Haroon PhD AMInstP Research Associate in MR Neuroimaging Division of Imaging Science and Biomedical Engineering Faculty of Medical and Human Sciences The University of Manchester Room G.603 Stopford Building, Oxford Road, Manchester M13 9PT England, United Kingdom Tel: +44 (0)161 275 6871 Fax: +44 (0)161 275 5145 Email: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Web: www.isbe.man.ac.uk/~hharoon http://www.isbe.man.ac.uk/~hharoon
[Fwd: Re: [caret-users] Macaque Neuroanatomy]
Passing on Jim Lewis' reply about Hamied's query, which DVE and Rolf Kotter also covered. Original Message Subject:Re: [caret-users] Macaque Neuroanatomy Date: Fri, 23 Mar 2007 15:49:10 -0400 From: James Lewis [EMAIL PROTECTED] To: Donna Dierker [EMAIL PROTECTED] References: [EMAIL PROTECTED] [EMAIL PROTECTED] Donna (others), The brain area acronyms below are largely derived from non-English terminology, typically German, and thus I didn't include the full names in some of those cases. However, my recollection is roughly: IPa = intraparietal, anterior PA = no idea TAa - is some temporal cortex subdivision, anterior TE, Tx = similarly are temporal subdivisions, but of unclear actual nomenclature. My experience in finding/using such terminology was that if some study had cited a reasonable looking homologue to what I was observing in our monkey slice sections then I would use their nomenclature. If there were competing potential names then I went with that which seemed closest to what I was seeing. In the case of these latter names, I couldn't find any more recent refernces, and thus stook with their nomenclature even though they didn't explicitly state what their acronyms stood for--often times these were transcribed from German or the like. The nomenclature issue was a BIG issue indeed, and will likely continue to evolve as newer and better methods of segregating brain regions develop. The problem only gets worse when dealing with human brain areas/regions. hope this helps. jim James W. Lewis, PhD. Dept. Physiology and Pharmacology West Virginia University PO Box 9229 Morgantown, WV 26506-9229 Phone: (304) 293-1517 Fax: (304) 293-3850 Email: [EMAIL PROTECTED] http://www.hsc.wvu.edu/wvucn/people/Lewis Donna Dierker [EMAIL PROTECTED] 3/22/2007 1:54 PM Hi Jim, Thought you might know the answer to this user's query; I don't, and DVE is out of the office. Donna On 03/22/2007 12:27 PM, Hamied Haroon wrote: Hello, Im not a neuroanatomist, but I want to find the neuroanatomical names for the temporal areas in the F99UA1 macaque parcellated according to C:\Caret5\CARET_TUTORIAL_SEPT06\MACAQUE\Macaque.F99UA1.BOTH.LewisVE00+orig Most of the abbreviations given in the associated paint colour key are listed explicitly in the LVE00 reference paper (Lewis JW and Van Essen DC, /J Comp Neurol/, *428*:112-37, 2000). Unfortunately the following abbreviations dont appear to be given in full in this reference paper or in the other references cited (Seltzer B and Pandya DN, /Brain Res/, *149*:1-24, 1978, and Cusick CG et al., /J Comp Neurol/, *360*:513-35, 1995): IPa PA TAa TE Ts I would be very grateful if anyone could please let me know what these abbreviations are in full. Many thanks in anticipation. Hamied Hamied Ahmad Haroon PhD AMInstP Research Associate in MR Neuroimaging Division of Imaging Science and Biomedical Engineering Faculty of Medical and Human Sciences The University of Manchester Room G.603 Stopford Building, Oxford Road, Manchester M13 9PT England, United Kingdom Tel: +44 (0)161 275 6871 Fax: +44 (0)161 275 5145 Email: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Web: www.isbe.man.ac.uk/~hharoon http://www.isbe.man.ac.uk/%7Ehharoon ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users -- Donna L. Dierker (Formerly Donna Hanlon; no change in marital status -- see http://home.att.net/~donna.hanlon for details.) -- Donna L. Dierker (Formerly Donna Hanlon; no change in marital status -- see http://home.att.net/~donna.hanlon for details.)
RE: [Fwd: Re: [caret-users] Macaque Neuroanatomy]
Hi Donna and James, Thanks very much for your kind replies. It can be quite annoying when you go to the source reference for the labeling acronym and still can't find what it actually stands for. I'm just glad I'm not the only one who finds this a big issue! Thanks for the warning about the human brain regions. Best wishes, Hamied -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Donna Dierker Sent: 23 March 2007 19:52 To: caret-users Cc: James Lewis Subject: [Fwd: Re: [caret-users] Macaque Neuroanatomy] Passing on Jim Lewis' reply about Hamied's query, which DVE and Rolf Kotter also covered. Original Message Subject:Re: [caret-users] Macaque Neuroanatomy Date: Fri, 23 Mar 2007 15:49:10 -0400 From: James Lewis [EMAIL PROTECTED] To: Donna Dierker [EMAIL PROTECTED] References: [EMAIL PROTECTED] [EMAIL PROTECTED] Donna (others), The brain area acronyms below are largely derived from non-English terminology, typically German, and thus I didn't include the full names in some of those cases. However, my recollection is roughly: IPa = intraparietal, anterior PA = no idea TAa - is some temporal cortex subdivision, anterior TE, Tx = similarly are temporal subdivisions, but of unclear actual nomenclature. My experience in finding/using such terminology was that if some study had cited a reasonable looking homologue to what I was observing in our monkey slice sections then I would use their nomenclature. If there were competing potential names then I went with that which seemed closest to what I was seeing. In the case of these latter names, I couldn't find any more recent refernces, and thus stook with their nomenclature even though they didn't explicitly state what their acronyms stood for--often times these were transcribed from German or the like. The nomenclature issue was a BIG issue indeed, and will likely continue to evolve as newer and better methods of segregating brain regions develop. The problem only gets worse when dealing with human brain areas/regions. hope this helps. jim James W. Lewis, PhD. Dept. Physiology and Pharmacology West Virginia University PO Box 9229 Morgantown, WV 26506-9229 Phone: (304) 293-1517 Fax: (304) 293-3850 Email: [EMAIL PROTECTED] http://www.hsc.wvu.edu/wvucn/people/Lewis Donna Dierker [EMAIL PROTECTED] 3/22/2007 1:54 PM Hi Jim, Thought you might know the answer to this user's query; I don't, and DVE is out of the office. Donna On 03/22/2007 12:27 PM, Hamied Haroon wrote: Hello, Im not a neuroanatomist, but I want to find the neuroanatomical names for the temporal areas in the F99UA1 macaque parcellated according to C:\Caret5\CARET_TUTORIAL_SEPT06\MACAQUE\Macaque.F99UA1.BOTH.LewisVE00+orig Most of the abbreviations given in the associated paint colour key are listed explicitly in the LVE00 reference paper (Lewis JW and Van Essen DC, /J Comp Neurol/, *428*:112-37, 2000). Unfortunately the following abbreviations dont appear to be given in full in this reference paper or in the other references cited (Seltzer B and Pandya DN, /Brain Res/, *149*:1-24, 1978, and Cusick CG et al., /J Comp Neurol/, *360*:513-35, 1995): IPa PA TAa TE Ts I would be very grateful if anyone could please let me know what these abbreviations are in full. Many thanks in anticipation. Hamied Hamied Ahmad Haroon PhD AMInstP Research Associate in MR Neuroimaging Division of Imaging Science and Biomedical Engineering Faculty of Medical and Human Sciences The University of Manchester Room G.603 Stopford Building, Oxford Road, Manchester M13 9PT England, United Kingdom Tel: +44 (0)161 275 6871 Fax: +44 (0)161 275 5145 Email: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Web: www.isbe.man.ac.uk/~hharoon http://www.isbe.man.ac.uk/%7Ehharoon ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users -- Donna L. Dierker (Formerly Donna Hanlon; no change in marital status -- see http://home.att.net/~donna.hanlon for details.) -- Donna L. Dierker (Formerly Donna Hanlon; no change in marital status -- see http://home.att.net/~donna.hanlon for details.) ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] Macaque Neuroanatomy
Hamied, The best source I know of for your questions is the CoCoMac database developed by Rolf Kotter and colleagues. http://cocomac.org/home.htm You have to get an account, but once you do, you can search for connections of any area of interest and then click on the area abbreviation to get a popup window showing the full name and reference. The results are: TA: Temporal area TA TE: Inferotemporal area TE PA#1: Postcentral area PA von Bonin, G; Bailey, P 1947 The Neocortex of Macaca Mulatta IPa: Intraparietal sulcus associated area in the superior temporal sulcus TAa: Temporal area TAa Seltzer, B; Pandya, DN 1978 Site Ts1: Area temporalis superior 1 Galaburda, AM; Pandya, DN 1983 The intrinsic architectonic and connectional organization of the superior temporal region of the rhesus monkey Site NeuroNames in BrainInfo (http://braininfo.rprc.washington.edu/) is another useful source of terminology information but doesn't yet have full entries for the ones you asked about. David Van Essen On Mar 22, 2007, at 12:27 PM, Hamied Haroon wrote: Hello, I’m not a neuroanatomist, but I want to find the neuroanatomical names for the temporal areas in the F99UA1 macaque parcellated according to C:\Caret5\CARET_TUTORIAL_SEPT06\MACAQUE \Macaque.F99UA1.BOTH.LewisVE00+orig Most of the abbreviations given in the associated paint colour key are listed explicitly in the “LVE00” reference paper (Lewis JW and Van Essen DC, J Comp Neurol, 428:112-37, 2000). Unfortunately the following abbreviations don’t appear to be given in full in this reference paper or in the other references cited (Seltzer B and Pandya DN, Brain Res, 149:1-24, 1978, and Cusick CG et al., J Comp Neurol, 360:513-35, 1995): IPa PA TAa TE Ts I would be very grateful if anyone could please let me know what these abbreviations are in full. Many thanks in anticipation. Hamied Hamied Ahmad Haroon PhD AMInstP Research Associate in MR Neuroimaging Division of Imaging Science and Biomedical Engineering Faculty of Medical and Human Sciences The University of Manchester Room G.603 Stopford Building, Oxford Road, Manchester M13 9PT England, United Kingdom Tel: +44 (0)161 275 6871 Fax: +44 (0)161 275 5145 Email: [EMAIL PROTECTED] Web: www.isbe.man.ac.uk/~hharoon ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
