[Brains-users] Re: Brains-users Digest, Vol 8, Issue 12
Cherie Marvel
cherie at psychiatry.uiowa.edu
Wed Feb 22 10:51:20 PST 2006
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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