[Brains-users] Re: Brains-users Digest, Vol 8, Issue 12
Eugene Zeien
eugene-zeien at uiowa.edu
Wed Feb 22 11:01:49 PST 2006
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
>>
>>
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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
>>*******************************************
>>
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