[Brains-users] BRAINS updates

Cherie Marvel cherie at psychiatry.uiowa.edu
Wed Feb 22 11:13:16 PST 2006 

Ben installed BRAINS towards the end of last summer onto my box. Looks
like I have:
brains2-RedHatEnterpriseWS4-20050830-035816

It's been running well, so if I don't have to change anything, maybe I
can just leave it?? Let me know what you think. thanks Gene!

On Feb 22, 2006 01:01 PM, Eugene Zeien <eugene-zeien at uiowa.edu> wrote:

> I do not know which version you currently have.
> Please run
>     rpm -qa brains*
> and reply with results.  Many people are using versions which are
> 1, 2, even 3 years old.  Our last "stable" release was
>    brains2-RedHatEnterpriseWS4-20050603-040809
> Of course, we have updated brains2 within the lab many times since
> then.
> Hoping to have a new "stable" release very, very soon. (it's overdue!)
> 
> Cherie Marvel wrote:
> > To the IPL Folks,
> > 
> > I've been hovering over the listserv reading e-mails in case
> > something
> > applies to me. Luckily things have been working fine, but I noticed
> > a
> > few references lately to a new version/updates in BRAINS. ARe there
> > new
> > releases, and if so, where can I find the downloads?
> > 
> > thanks, hope all is well! --cherie
> > 							
> > 
> > On Feb 22, 2006 12:00 PM, brains-users-request at psychiatry.uiowa.edu
> > wrote:
> > 
> > 
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> >>
> >>Today's Topics:
> >>
> >>   1. .brains2rc (Re: [Brains-users] Error message during
> >>      measurement of	T50 volumes) (Christoph Christmann)
> >>   2. Re: .brains2rc (Re: [Brains-users] Error message during
> >>      measurement	of	T50 volumes) (Eugene Zeien)
> >>   3. [Fwd: Re: Thalamic MD measures and greeting] (Hans Johnson)
> >>   4. RE: Thalamic MD measures and greeting (Ronald Pierson)
> >>
> >>
>
> >>>>----------------------------------------------------------------------
> >>
> >>Message: 1
> >>Date: Wed, 22 Feb 2006 10:24:47 +0100
> >>From: Christoph Christmann <christma at zi-mannheim.de>
> >>Subject: .brains2rc (Re: [Brains-users] Error message during
> >>	measurement of	T50 volumes)
> >>To: brains-users at psychiatry.uiowa.edu
> >>Message-ID: <6.2.5.6.2.20060222101119.02e818d0 at zi-mannheim.de>
> >>Content-Type: text/plain;	charset="us-ascii";	format=flowed
> >>
> >>Hi all,
> >>
> >>regarding the config files I noticed that the general config file
> >>(in
> >>/opt/brains2/bin) has a different syntax. Instead of
> >>
> >>
> >>
> >>>  B2_EVAL_TCL "B2_GLOBAL_DATA_DIR" "set B2_GLOBAL_DATA_DIR 
> >>>/raid0/data/new_data/brains2 ; "
> >>
> >>it seems to be necessary to use
> >>
> >>B2_GLOBAL_DATA_DIR /home/morpho/brains2_data
> >>
> >>Otherwise brains2 reports an error (unknown command...)
> >>
> >>However, setting the parameters as follows
> >>
> >># set directory where scripts are saved
> >>B2_WORK_DIR ${HOME}/morpho/scripts
> >># set global data directory
> >>B2_GLOBAL_DATA_DIR /home/morpho/brains2_data
> >># redirect brains2 meausres
> >>B2_SCV_FILE ${HOME}/data/Class_Volumes
> >>B2_SSM_FILE ${HOME}/data/Surface_Measures
> >>
> >>results in
> >>
> >>1. The first two commands are executed
> >>2. The last two commands result in error reports
> >>3. An additional error occures, e.g. the directory where the NET 
> >>information is stored (usually /opt/brains2/bin/net) could not be
> >>set.
> >>
> >>Therefore we abstained to use this configuration file so far. 
> >>Nevertheless, we would be happy to use a correct version in order to
> >>prevent the known error messages during the segmentation process.
> >>
> >>Thanks in advance for any hint
> >>
> >>Christoph
> >>
> >>
> >>>This line (if it weren't commented out) would configure where
> >>>brains2
> >>>scripts are stored.
> >>>
> >>># Default Location to place batch files
> >>># B2_EVAL_TCL "B2_WORK_DIR" "set B2_WORK_DIR ${HOME}/<username> ; "
> >>>
> >>>If you wish to change these for everyone using your computer,
> >>>edit /opt/brains2/bin/brains2rc. If you want to change these
> >>>settings
> >>>for yourself only,
> >>>  copy these lines into your ~/.brains2rc
> >>>  delete the # for the "B2_WORK_DIR" line
> >>>  and change to locations of your choice
> >>>
> >>>For example,
> >>>
> >>>  B2_EVAL_TCL "B2_GLOBAL_DATA_DIR" "set B2_GLOBAL_DATA_DIR 
> >>>/home/simone/brains2_data ; "
> >>>B2_EVAL_TCL "B2_WORK_DIR" "set B2_WORK_DIR /home/simone/scripts ; "
> >>>(might want to 'mkdir /volume/storage/location
> >>>/home/simone/scripts'
> >>>first) ;-)
> >>>
> >>>Simone Brockman wrote:
> >>>
> >>>>It seems I spoke too soon about not having any further problems...
> >>>>When I go to run the t50 volumes, I get an error message both when
> >>>>I save it to run later and if I try to run it straight away. The 
> >>>>error message when I try to save occurs after I try to save the 
> >>>>_t50vol.brains2 in the default location of the home directory and
> >>>>reads
> >>>>"Failed to save the check measurement script! Verify there that 
> >>>>there is a ...ACPC/root directory."
> >>>>and the error message when I try to run interactively occurs when
> >>>>I
> >>>>try to select the update button on the Check T50 Volumes dialogue
> >>>>box and reads
> >>>>"Failed to open global raw volume data 
> >>>>file  /raid0/data/new_data/brains2/t50/t50_volumes_raw.dat.
> >>>>I have the option to modify the Global Data File before running
> >>>>the
> >>>>T50 Volumes but it seems to be looking for something my system 
> >>>>doesn't have. Isn't /raid0 an IPL specific directory structure? Am
> >>>>I missing a file or have I done soemthing incorrectly in preceding
> >>>>steps??
> >>>>Many thanks for your advice
> >>>>Simone
> >>>>UWA Perth
> >>>>Western Australia
> >>>>
> >>>>_______________________________________________
> >>>>Brains-users mailing list
> >>>>Brains-users at www.psychiatry.uiowa.edu
> >>>>http://www.psychiatry.uiowa.edu/mailman/listinfo/brains-users
> >>>
> >>>_______________________________________________
> >>>Brains-users mailing list
> >>>Brains-users at www.psychiatry.uiowa.edu
> >>>http://www.psychiatry.uiowa.edu/mailman/listinfo/brains-users
> >>
> >>-- 
> >>Christoph Christmann                  christma at as200.zi-mannheim.de
> >>Psychologist, MEE                     Fon/Fax +49 621 1703 63 18/05
> >>Central Institute of Mental Health    http://www.zi-mannheim.de
> >>Department of Clinical                  D-68159 Mannheim J5
> >>and Cognitive Psychology                       
> >>
> >>
>
> >>>>**********************************************************************************************
> >>IMPORTANT: The contents of this email and any attachments are
> >>confidential. They are intended for the
> >>named recipient(s) only.
> >>If you have received this email in error, please notify the system
> >>manager or the sender immediately and do
> >>not disclose the contents to anyone or make copies thereof.
> >>*** eSafe scanned this email for viruses, vandals, and malicious
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>
> >>>>**********************************************************************************************
> >>
> >>
> >>
> >>------------------------------
> >>
> >>Message: 2
> >>Date: Wed, 22 Feb 2006 09:23:26 -0600
> >>From: Eugene Zeien <eugene-zeien at uiowa.edu>
> >>Subject: Re: .brains2rc (Re: [Brains-users] Error message during
> >>	measurement	of	T50 volumes)
> >>To: Christoph Christmann <christma at zi-mannheim.de>
> >>Cc: brains-users at psychiatry.uiowa.edu
> >>Message-ID: <43FC81EE.2000709 at uiowa.edu>
> >>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >>
> >>Ah.  You are using an older version of BRAINS.
> >>The syntax of the .brains2rc file changed in... January 2006?
> >>
> >>I do not see any evidence that the last 2 variables existed.
> >>B2_SCV_FILE, B2_SSM_FILE
> >>I think the best you can hope for is to set the directory where
> >>those data files are written with B2_GLOBAL_DATA_DIR
> >>
> >>Christoph Christmann wrote:
> >>
> >>>Hi all,
> >>>
> >>>regarding the config files I noticed that the general config file
> >>>(in
> >>>/opt/brains2/bin) has a different syntax. Instead of
> >>>
> >>>
> >>>
> >>>>  B2_EVAL_TCL "B2_GLOBAL_DATA_DIR" "set B2_GLOBAL_DATA_DIR 
> >>>>/raid0/data/new_data/brains2 ; "
> >>>
> >>>
> >>>it seems to be necessary to use
> >>>
> >>>B2_GLOBAL_DATA_DIR /home/morpho/brains2_data
> >>>
> >>>Otherwise brains2 reports an error (unknown command...)
> >>>
> >>>However, setting the parameters as follows
> >>>
> >>># set directory where scripts are saved
> >>>B2_WORK_DIR ${HOME}/morpho/scripts
> >>># set global data directory
> >>>B2_GLOBAL_DATA_DIR /home/morpho/brains2_data
> >>># redirect brains2 meausres
> >>>B2_SCV_FILE ${HOME}/data/Class_Volumes
> >>>B2_SSM_FILE ${HOME}/data/Surface_Measures
> >>>
> >>>results in
> >>>
> >>>1. The first two commands are executed
> >>>2. The last two commands result in error reports
> >>>3. An additional error occures, e.g. the directory where the NET 
> >>>information is stored (usually /opt/brains2/bin/net) could not be
> >>>set.
> >>>
> >>>Therefore we abstained to use this configuration file so far. 
> >>>Nevertheless, we would be happy to use a correct version in order
> >>>to
> >>>prevent the known error messages during the segmentation process.
> >>>
> >>>Thanks in advance for any hint
> >>>
> >>>Christoph
> >>>
> >>>
> >>>>This line (if it weren't commented out) would configure where
> >>>>brains2
> >>>>scripts are stored.
> >>>>
> >>>># Default Location to place batch files
> >>>># B2_EVAL_TCL "B2_WORK_DIR" "set B2_WORK_DIR ${HOME}/<username> ;
> >>>>"
> >>>>
> >>>>If you wish to change these for everyone using your computer,
> >>>>edit /opt/brains2/bin/brains2rc. If you want to change these
> >>>>settings
> >>>>for yourself only,
> >>>>  copy these lines into your ~/.brains2rc
> >>>>  delete the # for the "B2_WORK_DIR" line
> >>>>  and change to locations of your choice
> >>>>
> >>>>For example,
> >>>>
> >>>>  B2_EVAL_TCL "B2_GLOBAL_DATA_DIR" "set B2_GLOBAL_DATA_DIR 
> >>>>/home/simone/brains2_data ; "
> >>>>B2_EVAL_TCL "B2_WORK_DIR" "set B2_WORK_DIR /home/simone/scripts ;
> >>>>"
> >>>>(might want to 'mkdir /volume/storage/location
> >>>>/home/simone/scripts'
> >>>>first) ;-)
> >>>>
> >>>>Simone Brockman wrote:
> >>>>
> >>>>
> >>>>>It seems I spoke too soon about not having any further
> >>>>>problems...
> >>>>>When I go to run the t50 volumes, I get an error message both
> >>>>>when
> >>>>>I
> >>>>>save it to run later and if I try to run it straight away. The
> >>>>>error
> >>>>>message when I try to save occurs after I try to save the 
> >>>>>_t50vol.brains2 in the default location of the home directory and
> >>>>>reads
> >>>>>"Failed to save the check measurement script! Verify there that
> >>>>>there
> >>>>>is a ...ACPC/root directory."
> >>>>>and the error message when I try to run interactively occurs when
> >>>>>I
> >>>>>try to select the update button on the Check T50 Volumes dialogue
> >>>>>box
> >>>>>and reads
> >>>>>"Failed to open global raw volume data file  
> >>>>>/raid0/data/new_data/brains2/t50/t50_volumes_raw.dat.
> >>>>>I have the option to modify the Global Data File before running
> >>>>>the
> >>>>>T50 Volumes but it seems to be looking for something my system 
> >>>>>doesn't have. Isn't /raid0 an IPL specific directory structure?
> >>>>>Am
> >>>>>I
> >>>>>missing a file or have I done soemthing incorrectly in preceding
> >>>>>steps??
> >>>>>Many thanks for your advice
> >>>>>Simone
> >>>>>UWA Perth
> >>>>>Western Australia
> >>>>>
> >>>>>_______________________________________________
> >>>>>Brains-users mailing list
> >>>>>Brains-users at www.psychiatry.uiowa.edu
> >>>>>http://www.psychiatry.uiowa.edu/mailman/listinfo/brains-users
> >>>>
> >>>>
> >>>>_______________________________________________
> >>>>Brains-users mailing list
> >>>>Brains-users at www.psychiatry.uiowa.edu
> >>>>http://www.psychiatry.uiowa.edu/mailman/listinfo/brains-users
> >>>
> >>>
> >>
> >>
> >>------------------------------
> >>
> >>Message: 3
> >>Date: Wed, 22 Feb 2006 11:26:41 -0600
> >>From: Hans Johnson <hans-johnson at uiowa.edu>
> >>Subject: [Brains-users] [Fwd: Re: Thalamic MD measures and greeting]
> >>To: "brains-users at psychiatry.uiowa.edu"
> >>	<brains-users at psychiatry.uiowa.edu>
> >>Message-ID: <43FC9ED1.5090100 at uiowa.edu>
> >>Content-Type: text/plain; charset="iso-8859-1"
> >>
> >>Benedicto,
> >>
> >>I am forwarding this message to the
> >>brains-users at psychiatry.uiowa.edu
> >>list so that more qualified people may respond.
> >>
> >>Regards,
> >>Hans
> >>
> >>-------------- next part --------------
> >>An embedded message was scrubbed...
> >>From: "Benedicto Crespo Facorro" <bcfacorro at humv.es>
> >>Subject: RE: Thalamic MD measures and greeting
> >>Date: Wed, 22 Feb 2006 17:09:57 +0100
> >>Size: 3892
> >>Url:
>
> >>>>http://www.psychiatry.uiowa.edu/pipermail/brains-users/attachments/20060222/48250dbe/ThalamicMDmeasuresandgreeting-0001.eml
> >>
> >>------------------------------
> >>
> >>Message: 4
> >>Date: Wed, 22 Feb 2006 11:46:31 -0600
> >>From: "Ronald Pierson" <ronald-pierson at uiowa.edu>
> >>Subject: [Brains-users] RE: Thalamic MD measures and greeting
> >>To: "'Benedicto Crespo Facorro'" <bcfacorro at humv.es>,
> >>	<brains-users at psychiatry.uiowa.edu>
> >>Message-ID: <000a01c637d7$ea322910$bf5dff81 at pierson>
> >>Content-Type: text/plain;	charset="iso-8859-1"
> >>
> >>Hi, this is Ron Pierson. I trained the ANN on that structure, and it
> >>really
> >>was pretty poor with ICC of ~0.5.  The ANN method created as much
> >>variability in the data as there actually is in the sample. There
> >>just
> >>was
> >>too much variability in the probability maps, and too little
> >>contrast
> >>at the
> >>MD borders, so the ANN didn't have good information to start with.
> >>We
> >>just
> >>would not believe any findings that were based on that bad data.
> >>There
> >>are
> >>some other ANN structures that are also pretty bad, but they serve
> >>as
> >>a good
> >>starting place for editing, which we always like to do anyway. This
> >>is
> >>not
> >>the case for the MD. So, we decided not to release it. Really, I
> >>think
> >>the
> >>best at the moment would be a manual method, though it may be rather
> >>labor-intensive to get the experience needed to do it.
> >>
> >>I think we look forward to a couple of new methods in the next year
> >>or
> >>so
> >>that may do a much better job on some of these structures. I'm sure
> >>we
> >>will
> >>announce on this list when they become available.
> >>
> >>See you in Florence?
> >>
> >>Ron
> >>
> >>
> >>-----Original Message-----
> >>From: Benedicto Crespo Facorro [mailto:bcfacorro at humv.es] 
> >>Sent: Wednesday, February 22, 2006 10:10 AM
> >>To: hans-johnson at uiowa.edu
> >>Cc: RobertoRoiz
> >>Subject: RE: Thalamic MD measures and greeting
> >>
> >>Dear Hans, 
> >>
> >>My name is Benedicto Crespo-Facorro and I was a former postdoc at
> >>the
> >>IPL
> >>IC. 
> >>We are exploring thalamic volumes. We have obtained total thalamic
> >>volume.
> >>We are now trying to know whether it is possible to get automated
> >>measure
> >>(neuro net) of the Thalamic MD, as Ruth published in NI 2002.
> >>Could you help out us to find where is the option in BRAINS2 menu?
> >>
> >>Thanks for your time and interest,
> >>bn
> >>
> >>
> >>
> >>
> >>
> >>Ruth,
> >>Thanks and good luck with your research too!!
> >>bn
> >>
> >>-----Mensaje original-----
> >>De: Spinks, Ruth A [mailto:ruth-spinks at uiowa.edu] 
> >>Enviado el: miércoles, 22 de febrero de 2006 16:45
> >>Para: Benedicto Crespo Facorro
> >>Asunto: RE: Thalamic MD measures and greeting
> >>
> >>
> >>Bene,
> >>
> >>Good to hear from you and I'm glad to hear your imaging research is
> >>doing so
> >>well. I would suggest you ask Hans Johnson whether there is an MD
> >>neural
> >>net. I am no longer working in the CRC so I haven't been doing
> >>imaging
> >>for
> >>the last 3 years. I took over Remi Cadoret's adoption study and I
> >>work
> >>with
> >>Steve Arndt doing research on the cognitive effects of substance
> >>abuse
> >>and
> >>dependence.
> >>
> >>Good luck.
> >>Ruth
> >>
> >>-----Original Message-----
> >>From: Benedicto Crespo Facorro [mailto:bcfacorro at humv.es] 
> >>Sent: Wednesday, February 22, 2006 9:35 AM
> >>To: Spinks, Ruth A
> >>Cc: RobertoRoiz
> >>Subject: Thalamic MD measures and greeting
> >>
> >>Hi Ruth,
> >>Hope you are doing well and your research successful.
> >>As you may know we have been collected MRI in the last three years
> >>(FES).
> >>Just recently we started to analyze data. We found a decrease in
> >>total
> >>thalamic volume in FES (79) when comparing to healthy volunteers
> >>(45)
> >>.
> >>I read your paper in NI regarding the method. In that paper you
> >>described MD
> >>measures. Is this option (MD neuronet) available in BRAINS2 ?? We
> >>can
> >>not
> >>find it in the menu. Thanks a lot and warm hugs,
> >>
> >>Bene
> >>
> >>Benedicto Crespo-Facorro MD,
> >>Schizophrenia Research Program
> >>Dep. of  Psychiatry. Pabellón 20.
> >>HU Marqués de Valdecilla
> >>39008 Santander
> >>Spain 
> >>
> >>
> >>
> >>
> >>
> >>
> >>------------------------------
> >>
> >>_______________________________________________
> >>Brains-users mailing list
> >>Brains-users at www.psychiatry.uiowa.edu
> >>http://www.psychiatry.uiowa.edu/mailman/listinfo/brains-users
> >>
> >>
> >>End of Brains-users Digest, Vol 8, Issue 12
> >>*******************************************
> >>
> > 
> > 
> > 
> > _______________________________________________
> > Brains-users mailing list
> > Brains-users at www.psychiatry.uiowa.edu
> > http://www.psychiatry.uiowa.edu/mailman/listinfo/brains-users
> > 
>

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