From jason at bic.mni.mcgill.ca  Sun Feb  3 18:18:10 2008
From: jason at bic.mni.mcgill.ca (Jason Lerch)
Date: Sun, 3 Feb 2008 18:18:10 -0500
Subject: [MINC-users] RMINC v0.4
Message-ID: <9f345c5b330a56021bfa067eabee0f4b@bic.mni.mcgill.ca>

Greetings all,

RMINC v0.4 is available for those who care. A quick summary of what's 
new:

* easier to use linear models and file writing utilities.
* descriptive statistics (mean, standard deviation, etc.) that can be 
split by random groupings.
* better incorporation of False Discovery Rate thresholding.

(For those who've never heard of RMINC: it is a package to allow 
voxel-wise statistics to be performed inside R, an open source 
statistics program/toolbox).

The code is available here:

https://code.launchpad.net/rminc/1.0/0.4

To install, download the tarball, and run 'R CMD INSTALL 
RMINC_0.4.tar.gz --configure-args=/path/to/minc2' If you want to 
install it a nondefault location, set the R_LIBS environment variable 
first.

You'll also find a PDF file in the same place which is an early stage 
version of a mini-booklet describing how to use RMINC. Plenty of 
examples in there to help you get started, though the actual text is 
still, um, rather incomplete.

The RMINC project is now hosted on Ubuntu's launchpad site:

https://launchpad.net/rminc

There are tools there for asking questions, reporting bugs, and 
suggesting blue-prints for wanted functionality. Please do use them - 
I'd love to hear about bugs and am quite happy to listen to suggestions 
(i.e. blueprints) for what RMINC should be able to do. Though I won't 
promise to get it all done by tomorrow!

For all those MINC developers out there: how about moving some of the 
other public MINC tools and libraries to launchpad? Seems to make code 
sharing, bug reporting, etc. quite easy without requiring us to 
reinvent the wheel on some server in Montreal. Thoughts?

Cheers,

Jason


From nikelski at bic.mni.mcgill.ca  Tue Feb  5 16:29:41 2008
From: nikelski at bic.mni.mcgill.ca (EJ Nikelski)
Date: Tue, 5 Feb 2008 16:29:41 -0500
Subject: [MINC-users] RMINC v0.4
In-Reply-To: <9f345c5b330a56021bfa067eabee0f4b@bic.mni.mcgill.ca>
References: <9f345c5b330a56021bfa067eabee0f4b@bic.mni.mcgill.ca>
Message-ID: <e12172550802051329w632e0cd4kaba33e29afc73463@mail.gmail.com>

Thanks Jason,

    Building RMINC on my MacBook, I found a couple of things that
might be worth noting:

(1) Make sure that your minc libraries are built as shared/dynamic ...
as R needs to be able to load the minc2 library dynamically.  Note the
the hdf5 and netcdf libs also need to be dynamic, else the configure
script complains and falls over.  This caught me, as I like to build
only static libs ... which I will now stop doing.

(2) I had better luck installing the package with the following:

>>R CMD INSTALL --configure-args='--with-build-path=/path/to/minc2
--enable-minc2' RMINC_0.4.tar.gz

Cheers,

-Jim



On Feb 3, 2008 6:18 PM, Jason Lerch <jason at bic.mni.mcgill.ca> wrote:
> Greetings all,
>
> RMINC v0.4 is available for those who care. A quick summary of what's
> new:
>
> * easier to use linear models and file writing utilities.
> * descriptive statistics (mean, standard deviation, etc.) that can be
> split by random groupings.
> * better incorporation of False Discovery Rate thresholding.
>
> (For those who've never heard of RMINC: it is a package to allow
> voxel-wise statistics to be performed inside R, an open source
> statistics program/toolbox).
>
> The code is available here:
>
> https://code.launchpad.net/rminc/1.0/0.4
>
> To install, download the tarball, and run 'R CMD INSTALL
> RMINC_0.4.tar.gz --configure-args=/path/to/minc2' If you want to
> install it a nondefault location, set the R_LIBS environment variable
> first.
>
> You'll also find a PDF file in the same place which is an early stage
> version of a mini-booklet describing how to use RMINC. Plenty of
> examples in there to help you get started, though the actual text is
> still, um, rather incomplete.
>
> The RMINC project is now hosted on Ubuntu's launchpad site:
>
> https://launchpad.net/rminc
>
> There are tools there for asking questions, reporting bugs, and
> suggesting blue-prints for wanted functionality. Please do use them -
> I'd love to hear about bugs and am quite happy to listen to suggestions
> (i.e. blueprints) for what RMINC should be able to do. Though I won't
> promise to get it all done by tomorrow!
>
> For all those MINC developers out there: how about moving some of the
> other public MINC tools and libraries to launchpad? Seems to make code
> sharing, bug reporting, etc. quite easy without requiring us to
> reinvent the wheel on some server in Montreal. Thoughts?
>
> Cheers,
>
> Jason
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From jason at bic.mni.mcgill.ca  Tue Feb  5 17:09:14 2008
From: jason at bic.mni.mcgill.ca (Jason Lerch)
Date: Tue, 5 Feb 2008 17:09:14 -0500
Subject: [MINC-users] RMINC v0.4
In-Reply-To: <e12172550802051329w632e0cd4kaba33e29afc73463@mail.gmail.com>
References: <9f345c5b330a56021bfa067eabee0f4b@bic.mni.mcgill.ca>
Message-ID: <47A8DE8A.5090009@bic.mni.mcgill.ca>

Hello Jim (and others),

you're right, the libraries need to be compiled as dynamic libs (or with 
the -fPIC option to GCC if you really want them static). As for the 
second part - I thought I had fixed the necessity for '--enable-minc2', 
but it looks like I was wrong. I'll check and fix that - thanks for 
pointing it out.

Cheers,

Jason

EJ Nikelski wrote:
> Thanks Jason,
>
>     Building RMINC on my MacBook, I found a couple of things that
> might be worth noting:
>
> (1) Make sure that your minc libraries are built as shared/dynamic ...
> as R needs to be able to load the minc2 library dynamically.  Note the
> the hdf5 and netcdf libs also need to be dynamic, else the configure
> script complains and falls over.  This caught me, as I like to build
> only static libs ... which I will now stop doing.
>
> (2) I had better luck installing the package with the following:
>
>   
>>> R CMD INSTALL --configure-args='--with-build-path=/path/to/minc2
>>>       
> --enable-minc2' RMINC_0.4.tar.gz
>
> Cheers,
>
> -Jim
>
>
>
> On Feb 3, 2008 6:18 PM, Jason Lerch <jason at bic.mni.mcgill.ca> wrote:
>   
>> Greetings all,
>>
>> RMINC v0.4 is available for those who care. A quick summary of what's
>> new:
>>
>> * easier to use linear models and file writing utilities.
>> * descriptive statistics (mean, standard deviation, etc.) that can be
>> split by random groupings.
>> * better incorporation of False Discovery Rate thresholding.
>>
>> (For those who've never heard of RMINC: it is a package to allow
>> voxel-wise statistics to be performed inside R, an open source
>> statistics program/toolbox).
>>
>> The code is available here:
>>
>> https://code.launchpad.net/rminc/1.0/0.4
>>
>> To install, download the tarball, and run 'R CMD INSTALL
>> RMINC_0.4.tar.gz --configure-args=/path/to/minc2' If you want to
>> install it a nondefault location, set the R_LIBS environment variable
>> first.
>>
>> You'll also find a PDF file in the same place which is an early stage
>> version of a mini-booklet describing how to use RMINC. Plenty of
>> examples in there to help you get started, though the actual text is
>> still, um, rather incomplete.
>>
>> The RMINC project is now hosted on Ubuntu's launchpad site:
>>
>> https://launchpad.net/rminc
>>
>> There are tools there for asking questions, reporting bugs, and
>> suggesting blue-prints for wanted functionality. Please do use them -
>> I'd love to hear about bugs and am quite happy to listen to suggestions
>> (i.e. blueprints) for what RMINC should be able to do. Though I won't
>> promise to get it all done by tomorrow!
>>
>> For all those MINC developers out there: how about moving some of the
>> other public MINC tools and libraries to launchpad? Seems to make code
>> sharing, bug reporting, etc. quite easy without requiring us to
>> reinvent the wheel on some server in Montreal. Thoughts?
>>
>> Cheers,
>>
>> Jason
>>
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>>     
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>   


From penhunelab at gmail.com  Thu Feb  7 09:44:47 2008
From: penhunelab at gmail.com (Penhune Lab)
Date: Thu, 7 Feb 2008 09:44:47 -0500
Subject: [MINC-users] EMMA for minc2
In-Reply-To: <d747ed50801102036k788725b1of5dad5b62afbc6de@mail.gmail.com>
References: <200801110214.m0B2EPNk6545313@yorick.bic.mni.mcgill.ca>
	<d747ed50801102036k788725b1of5dad5b62afbc6de@mail.gmail.com>
Message-ID: <c983d2410802070644m76475133h5b4048d6c351d1d3@mail.gmail.com>

I downloaded and compiled the emma source for minc2 in a mac workstation (
10.4.11)  and encountered only one problem that can easily be fixed:

includeblood.c:14:20: error: malloc.h: No such file or directory

I fixed the problem following this forum thread
http://forums.macosxhints.com/archive/index.php/t-2023.html

apparently malloc.h is deprecated in mac os (i don't know if this is true in
linux) and the best way to fix it to avoid breaking it for other platforms
is to change in includeblood.c

#include <malloc.h>

to

#if !defined(__APPLE__)
#include <malloc.h>
#endif

hope this helps towards a stable release of emma,

Alejandro Endo

On Jan 10, 2008 11:36 PM, Andrew Janke <a.janke at gmail.com> wrote:

> On Jan 11, 2008 1:14 PM, Claude LEPAGE <claude at bic.mni.mcgill.ca> wrote:
>
> > At last, I ported EMMA to minc2. I placed a temporary package
> > on my web page at:
> >
> > http://www.bic.mni.mcgill.ca/users/claude/emma-0.9.9.tar.gz
> >
> > Of course, I'm looking for feedback before the official release.
> > There are instructions on how to build the package in the README
> > file in the package. I hope it's clear enough and that everything
> > works.
>
> Thanks for all your work on this Claude,
>
> Users of this package might be interested to note that this version
> includes a fix such
>  that the max number of readable/writeable slices is now set to 1024
> as opposed to 160/256.
> This bug was noted by Mike on minc-users a little while ago.
>
> Once this new package has undergone a bit of testing it will be moved
> to http://packages.bic.mni.mcgill.ca/tgz
>
> Thanks again Claude,
>
>
> a
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



-- 
Laboratory for Motor Learning and Neural Plasticity
Directed by Dr. Virginia Penhune
Department of Psychology, Concordia University
SP-A 244, 7141 Sherbrooke St. W
Montreal, QC  H4B 1R6  Canada
(514)848-2424 ext. 7567
http://psychology.concordia.ca/fac/penhune/winindex.html

From a.janke at gmail.com  Thu Feb  7 22:22:06 2008
From: a.janke at gmail.com (Andrew Janke)
Date: Fri, 8 Feb 2008 14:22:06 +1100
Subject: [MINC-users] EMMA for minc2
In-Reply-To: <c983d2410802070644m76475133h5b4048d6c351d1d3@mail.gmail.com>
References: <200801110214.m0B2EPNk6545313@yorick.bic.mni.mcgill.ca>
	<d747ed50801102036k788725b1of5dad5b62afbc6de@mail.gmail.com>
	<c983d2410802070644m76475133h5b4048d6c351d1d3@mail.gmail.com>
Message-ID: <d747ed50802071922p371c709co48411dc4c884a81b@mail.gmail.com>

On Feb 8, 2008 1:44 AM, Penhune Lab <penhunelab at gmail.com> wrote:
> I downloaded and compiled the emma source for minc2 in a mac workstation (
> 10.4.11)  and encountered only one problem that can easily be fixed:
>
> includeblood.c:14:20: error: malloc.h: No such file or directory

Thanks for pointing this out Alejandro, I have taken the "scorched
earth" approach and just removed it. including malloc.h is somewhat
redundant now if you are including stdlib.h

I have comited the change to CVS.

Thanks again,


-- 
Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883

From alex at bic.mni.mcgill.ca  Wed Feb 13 22:16:55 2008
From: alex at bic.mni.mcgill.ca (Alex Zijdenbos)
Date: Wed, 13 Feb 2008 22:16:55 -0500
Subject: [MINC-users] RMINC v0.4
In-Reply-To: <9f345c5b330a56021bfa067eabee0f4b@bic.mni.mcgill.ca>
References: <9f345c5b330a56021bfa067eabee0f4b@bic.mni.mcgill.ca>
Message-ID: <e758a6650802131916u1c5af043k5a800ce5358622b6@mail.gmail.com>

Hi Jason,

There appear to be a few glitches with the configure/build process of
this version revolving around libz - I belief Claude will get in touch
with you to fix these.

As for the repository, some folks at the BIC (somehow including me)
have started to use Google Code for projects. I can't judge the
relative merits of this vs launchpad at the moment, but perhaps others
have thoughts? Using one of these types of services makes sense to me,
but if that is where we want to go it would also be nice to
standardize on one.

-- A

On Feb 3, 2008 6:18 PM, Jason Lerch <jason at bic.mni.mcgill.ca> wrote:
> Greetings all,
>
> RMINC v0.4 is available for those who care. A quick summary of what's
> new:
>
> * easier to use linear models and file writing utilities.
> * descriptive statistics (mean, standard deviation, etc.) that can be
> split by random groupings.
> * better incorporation of False Discovery Rate thresholding.
>
> (For those who've never heard of RMINC: it is a package to allow
> voxel-wise statistics to be performed inside R, an open source
> statistics program/toolbox).
>
> The code is available here:
>
> https://code.launchpad.net/rminc/1.0/0.4
>
> To install, download the tarball, and run 'R CMD INSTALL
> RMINC_0.4.tar.gz --configure-args=/path/to/minc2' If you want to
> install it a nondefault location, set the R_LIBS environment variable
> first.
>
> You'll also find a PDF file in the same place which is an early stage
> version of a mini-booklet describing how to use RMINC. Plenty of
> examples in there to help you get started, though the actual text is
> still, um, rather incomplete.
>
> The RMINC project is now hosted on Ubuntu's launchpad site:
>
> https://launchpad.net/rminc
>
> There are tools there for asking questions, reporting bugs, and
> suggesting blue-prints for wanted functionality. Please do use them -
> I'd love to hear about bugs and am quite happy to listen to suggestions
> (i.e. blueprints) for what RMINC should be able to do. Though I won't
> promise to get it all done by tomorrow!
>
> For all those MINC developers out there: how about moving some of the
> other public MINC tools and libraries to launchpad? Seems to make code
> sharing, bug reporting, etc. quite easy without requiring us to
> reinvent the wheel on some server in Montreal. Thoughts?
>
> Cheers,
>
> Jason
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>

From jason at bic.mni.mcgill.ca  Wed Feb 13 22:31:38 2008
From: jason at bic.mni.mcgill.ca (Jason Lerch)
Date: Wed, 13 Feb 2008 22:31:38 -0500
Subject: [MINC-users] RMINC v0.4
In-Reply-To: <e758a6650802131916u1c5af043k5a800ce5358622b6@mail.gmail.com>
References: <9f345c5b330a56021bfa067eabee0f4b@bic.mni.mcgill.ca>
	<e758a6650802131916u1c5af043k5a800ce5358622b6@mail.gmail.com>
Message-ID: <527B3E19-F16C-4744-B167-330F880FE46B@bic.mni.mcgill.ca>

Hi Alex and others,


On 13-Feb-08, at 10:16 PM, Alex Zijdenbos wrote:

> Hi Jason,
>
> There appear to be a few glitches with the configure/build process of
> this version revolving around libz - I belief Claude will get in touch
> with you to fix these.

OK, great.

>
> As for the repository, some folks at the BIC (somehow including me)
> have started to use Google Code for projects. I can't judge the
> relative merits of this vs launchpad at the moment, but perhaps others
> have thoughts? Using one of these types of services makes sense to me,
> but if that is where we want to go it would also be nice to
> standardize on one.

Google code was my second choice. The reasons why I opted for  
launchpad were the following:

* Bazaar rather than subversion: it makes it easier for somebody to  
contribute code without being given write access to the central  
repository. I.e. I can branch the code, make my changes (committing  
to my branch as needed), write them back to my own space on  
launchpad.net, and then register them with the project. The owners of  
the project can then decide to merge those changes at their leisure.  
Even if the owners don't merge immediately my branch will be listed  
with the project as one of the branches were work is ongoing. Of  
course creating patches, etc., is possible with subversion too, but  
the process is not as convenient.
* The "ask a question facility" is really nice - anyone who is  
registered to receive questions with a project will get them emailed,  
and they can answer by email, which in turn will show up on the web- 
site under that question.
* Ditto for blueprints - makes planning features and requesting  
features pretty easy, and, importantly, makes it trivial to  
communicate to the outside world what is planned for each particular  
project.
* The ability to group separate projects - i.e. various MINC tools  
could exist in separate projects but be grouped under one larger MINC  
meta-project.
* integration with debian/ubuntu packaging. Andrew liked this reason  
in particular, given that debian packages appear to be our most  
reliable binary packaging system at the moment.

Those are some of my reasons - but that being said, I agree that it's  
better to standardize on one place, and if the consensus is for  
google code or something else I'm willing to follow along.

Cheers,

Jason


>
> -- A
>
> On Feb 3, 2008 6:18 PM, Jason Lerch <jason at bic.mni.mcgill.ca> wrote:
>> Greetings all,
>>
>> RMINC v0.4 is available for those who care. A quick summary of what's
>> new:
>>
>> * easier to use linear models and file writing utilities.
>> * descriptive statistics (mean, standard deviation, etc.) that can be
>> split by random groupings.
>> * better incorporation of False Discovery Rate thresholding.
>>
>> (For those who've never heard of RMINC: it is a package to allow
>> voxel-wise statistics to be performed inside R, an open source
>> statistics program/toolbox).
>>
>> The code is available here:
>>
>> https://code.launchpad.net/rminc/1.0/0.4
>>
>> To install, download the tarball, and run 'R CMD INSTALL
>> RMINC_0.4.tar.gz --configure-args=/path/to/minc2' If you want to
>> install it a nondefault location, set the R_LIBS environment variable
>> first.
>>
>> You'll also find a PDF file in the same place which is an early stage
>> version of a mini-booklet describing how to use RMINC. Plenty of
>> examples in there to help you get started, though the actual text is
>> still, um, rather incomplete.
>>
>> The RMINC project is now hosted on Ubuntu's launchpad site:
>>
>> https://launchpad.net/rminc
>>
>> There are tools there for asking questions, reporting bugs, and
>> suggesting blue-prints for wanted functionality. Please do use them -
>> I'd love to hear about bugs and am quite happy to listen to  
>> suggestions
>> (i.e. blueprints) for what RMINC should be able to do. Though I won't
>> promise to get it all done by tomorrow!
>>
>> For all those MINC developers out there: how about moving some of the
>> other public MINC tools and libraries to launchpad? Seems to make  
>> code
>> sharing, bug reporting, etc. quite easy without requiring us to
>> reinvent the wheel on some server in Montreal. Thoughts?
>>
>> Cheers,
>>
>> Jason
>>
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users


From forrest.bao at gmail.com  Thu Feb 14 13:28:08 2008
From: forrest.bao at gmail.com (Forrest Sheng Bao)
Date: Thu, 14 Feb 2008 12:28:08 -0600
Subject: [MINC-users] any epileptic patient or common people's EEG data?
Message-ID: <889df5f00802141028l12e69024t91bcafffd13e2ffb@mail.gmail.com>

Hi guys,

Do you know have any EEG data of epileptic patients or common people? Or, do
you know any such data that are public and free ?

I am looking around to find some for my research. I want EEG data from both
epileptic patients or common people, so that I can compare features of both
kinds.

I wish i can find some free and public data. If you can let me know, I will
very grateful.

If you have some private data, please feel free to let me know, I can
discuss details about cooperations with you.

Thanks all,
Forrest

-- 
Forrest Sheng Bao
Ph.D. student, Dept. of Computer Science
M.Sc. student, Dept. of Electrical & Computer Engineering
Texas Tech University, USA
http://fsbao.net
1-806-577-4592

Forrest is an equal opportunity Email sender.
1. You are encouraged to use the language you prefer. Beyond English, I can
also read traditional/simplified Chinese and a bit German.
2. I will only send you files that can be opened by free or open source
software.

From john at absherneurology.com  Mon Feb 18 10:27:12 2008
From: john at absherneurology.com (John Absher)
Date: Mon, 18 Feb 2008 10:27:12 -0500
Subject: [MINC-users] ROI stats
In-Reply-To: <mailman.5.1203094815.33755.minc-users@bic.mni.mcgill.ca>
Message-ID: <LDECIOJNCEPJFCAHFLCCIEMACDAA.john@absherneurology.com>

Awhile ago, I posted a query on getting ROI values for the following
experiment:

4 subjects, each had baseline CBF PET scans x 2, then they had
low-blood-pressure CBF PET scans x 2.

I have run the SPM2 analysis, but I also wanted to look at the ROIs.  I have
data for 115 ROIS, for each of the 4 PET scans obtained for each of the 4
subjects.

What is the best statistic and correction method to use for evaluating the
significance of the regional changes in CBF when baseline measures are
compared to low-BP measures?

Thanks,

John

-----Original Message-----
From: minc-users-bounces at bic.mni.mcgill.ca
[mailto:minc-users-bounces at bic.mni.mcgill.ca]On Behalf Of
minc-users-request at bic.mni.mcgill.ca
Sent: Friday, February 15, 2008 12:00 PM
To: minc-users at bic.mni.mcgill.ca
Subject: MINC-users Digest, Vol 31, Issue 5


Send MINC-users mailing list submissions to
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Today's Topics:

   1. any epileptic patient or common people's EEG data?
      (Forrest Sheng Bao)


----------------------------------------------------------------------

Message: 1
Date: Thu, 14 Feb 2008 12:28:08 -0600
From: "Forrest Sheng Bao" <forrest.bao at gmail.com>
Subject: [MINC-users] any epileptic patient or common people's EEG
	data?
To: "MINC users mailing list" <MINC-users at bic.mni.mcgill.ca>
Message-ID:
	<889df5f00802141028l12e69024t91bcafffd13e2ffb at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

Hi guys,

Do you know have any EEG data of epileptic patients or common people? Or, do
you know any such data that are public and free ?

I am looking around to find some for my research. I want EEG data from both
epileptic patients or common people, so that I can compare features of both
kinds.

I wish i can find some free and public data. If you can let me know, I will
very grateful.

If you have some private data, please feel free to let me know, I can
discuss details about cooperations with you.

Thanks all,
Forrest

--
Forrest Sheng Bao
Ph.D. student, Dept. of Computer Science
M.Sc. student, Dept. of Electrical & Computer Engineering
Texas Tech University, USA
http://fsbao.net
1-806-577-4592

Forrest is an equal opportunity Email sender.
1. You are encouraged to use the language you prefer. Beyond English, I can
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End of MINC-users Digest, Vol 31, Issue 5
*****************************************



From jammam2 at yahoo.com  Thu Feb 21 12:32:14 2008
From: jammam2 at yahoo.com (Jamila Ahdidan)
Date: Thu, 21 Feb 2008 09:32:14 -0800 (PST)
Subject: [MINC-users] linear and non linear in the jacobian
In-Reply-To: <LDECIOJNCEPJFCAHFLCCIEMACDAA.john@absherneurology.com>
Message-ID: <15824.10312.qm@web65505.mail.ac4.yahoo.com>

Dear all,
  Here is a question that has given me some troubles, and I have seen that SPM5 solves the issue, but what about minc???
  Here it comes,
  I am interested in accounting for the linear (12 parameters) and non linear transformations in the determinant of the jacobian in order to measure all the differences between groups. It seems like SPM5 can do this, but how can I do it with minc. I know that the determinant of the jacobian can be calculated applying "mincblob -determinant" to the grid file (accounting only for the non-linear normalization). The question is how can I calculate the determinant for both the linear and non-linear normalization?
   
  I hope my question is clear and that someone somewhere has an answer to it. 
   
  Many regards,
  Jamila

       
---------------------------------
Be a better friend, newshound, and know-it-all with Yahoo! Mobile.  Try it now.

From jason at bic.mni.mcgill.ca  Thu Feb 21 13:09:47 2008
From: jason at bic.mni.mcgill.ca (Jason Lerch)
Date: Thu, 21 Feb 2008 13:09:47 -0500
Subject: [MINC-users] linear and non linear in the jacobian
In-Reply-To: <15824.10312.qm@web65505.mail.ac4.yahoo.com>
References: <15824.10312.qm@web65505.mail.ac4.yahoo.com>
Message-ID: <47BDBE6B.5040800@bic.mni.mcgill.ca>

Hello Jamila,

we do that in the following way:

1) compute the non-linear transform.
2) extract the linear part of that transform (using lin_from_nlin)
3) compute the displacement for each transform (using minc_displacement)
4) subtract the two displacement volumes to give you the pure non-linear 
displacement.
5) compute the Jacobian for the linear and pure-nonlinear displacement 
volumes.

Two of those bits of code are not yet circulating widely, but I'd be 
happy to send them to you if you'd like.

Cheers,

Jason

Jamila Ahdidan wrote:
> Dear all,
>   Here is a question that has given me some troubles, and I have seen that SPM5 solves the issue, but what about minc???
>   Here it comes,
>   I am interested in accounting for the linear (12 parameters) and non linear transformations in the determinant of the jacobian in order to measure all the differences between groups. It seems like SPM5 can do this, but how can I do it with minc. I know that the determinant of the jacobian can be calculated applying "mincblob -determinant" to the grid file (accounting only for the non-linear normalization). The question is how can I calculate the determinant for both the linear and non-linear normalization?
>    
>   I hope my question is clear and that someone somewhere has an answer to it. 
>    
>   Many regards,
>   Jamila
>
>        
> ---------------------------------
> Be a better friend, newshound, and know-it-all with Yahoo! Mobile.  Try it now.
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>   


From penhunelab at gmail.com  Thu Feb 21 13:58:00 2008
From: penhunelab at gmail.com (Penhune Lab)
Date: Thu, 21 Feb 2008 13:58:00 -0500
Subject: [MINC-users] EMMA for minc2
In-Reply-To: <d747ed50802071922p371c709co48411dc4c884a81b@mail.gmail.com>
References: <200801110214.m0B2EPNk6545313@yorick.bic.mni.mcgill.ca>
	<d747ed50801102036k788725b1of5dad5b62afbc6de@mail.gmail.com>
	<c983d2410802070644m76475133h5b4048d6c351d1d3@mail.gmail.com>
	<d747ed50802071922p371c709co48411dc4c884a81b@mail.gmail.com>
Message-ID: <c983d2410802211058m398a8c9i736fb7769d0a6ea@mail.gmail.com>

I am getting this output with fmrilm (mac, osx 10.4, emma 0.9.9) - the
function still completes normally but is this normal? I checked my contrast
output files with mincinfo - attvalue for the df and fwhm values and they
seem to have been written to the files... any ideas?

Thanks!
Chris

------------------------------------------------------
At the fmrilm level

df =

    resid: 244
      cor: 292
        t: [100 101 105 102 104]


Second_pass_slice =

     1

*(from micreate_group_variable): Variable 'df' is not a standard MINC
variable
micreate_group_variable: MINC package entry point
(from micreate_group_variable): Variable 'fwhm' is not a standard MINC
variable
micreate_group_variable: MINC package entry point*

[... repeated 28 more times]

Second_pass_slice =

     2

*(from micreate_group_variable): Variable 'df' is not a standard MINC
variable
micreate_group_variable: MINC package entry point
(from micreate_group_variable): Variable 'fwhm' is not a standard MINC
variable
micreate_group_variable: MINC package entry point*

Second_pass_slice =

     3

[no warning messages from here on]

On Thu, Feb 7, 2008 at 10:22 PM, Andrew Janke <a.janke at gmail.com> wrote:

> On Feb 8, 2008 1:44 AM, Penhune Lab <penhunelab at gmail.com> wrote:
> > I downloaded and compiled the emma source for minc2 in a mac workstation
> (
> > 10.4.11)  and encountered only one problem that can easily be fixed:
> >
> > includeblood.c:14:20: error: malloc.h: No such file or directory
>
> Thanks for pointing this out Alejandro, I have taken the "scorched
> earth" approach and just removed it. including malloc.h is somewhat
> redundant now if you are including stdlib.h
>
> I have comited the change to CVS.
>
> Thanks again,
>
>
> --
> Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Canberra->Australia    +61 (402) 700 883
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



-- 
Laboratory for Motor Learning and Neural Plasticity
Directed by Dr. Virginia Penhune
Department of Psychology, Concordia University
SP-A 244, 7141 Sherbrooke St. W
Montreal, QC H4B 1R6 Canada
(514)848-2424 ext. 7567
http://psychology.concordia.ca/fac/penhune/winindex.html

From a.janke at gmail.com  Thu Feb 21 16:06:38 2008
From: a.janke at gmail.com (Andrew Janke)
Date: Fri, 22 Feb 2008 08:06:38 +1100
Subject: [MINC-users] EMMA for minc2
In-Reply-To: <d747ed50802071922p371c709co48411dc4c884a81b@mail.gmail.com>
References: <200801110214.m0B2EPNk6545313@yorick.bic.mni.mcgill.ca>
	<d747ed50801102036k788725b1of5dad5b62afbc6de@mail.gmail.com>
	<c983d2410802070644m76475133h5b4048d6c351d1d3@mail.gmail.com>
	<d747ed50802071922p371c709co48411dc4c884a81b@mail.gmail.com>
Message-ID: <d747ed50802211306i35c4d822k2286ecf2e352f03b@mail.gmail.com>

Hi,

These "are not a standard variable" are largely innocuous and
something that I plan to remove from future versions of MINC2. At the
time I guess it seemed like a good idea to inform users that they were
using non-standard variables. This in itself should not cause
problems.


a

On Fri, Feb 8, 2008 at 2:22 PM, Andrew Janke <a.janke at gmail.com> wrote:
> On Feb 8, 2008 1:44 AM, Penhune Lab <penhunelab at gmail.com> wrote:
>  > I downloaded and compiled the emma source for minc2 in a mac workstation (
>  > 10.4.11)  and encountered only one problem that can easily be fixed:
>  >
>  > includeblood.c:14:20: error: malloc.h: No such file or directory
>
>  Thanks for pointing this out Alejandro, I have taken the "scorched
>  earth" approach and just removed it. including malloc.h is somewhat
>  redundant now if you are including stdlib.h
>
>  I have comited the change to CVS.
>
>  Thanks again,
>
>
>  --
>  Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
>  Canberra->Australia    +61 (402) 700 883
>



-- 
Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia +61 (402) 700 883

From a.janke at gmail.com  Fri Feb 22 06:55:07 2008
From: a.janke at gmail.com (Andrew Janke)
Date: Fri, 22 Feb 2008 22:55:07 +1100
Subject: [MINC-users] ROI stats
In-Reply-To: <LDECIOJNCEPJFCAHFLCCIEMACDAA.john@absherneurology.com>
References: <mailman.5.1203094815.33755.minc-users@bic.mni.mcgill.ca>
	<LDECIOJNCEPJFCAHFLCCIEMACDAA.john@absherneurology.com>
Message-ID: <d747ed50802220355r62418b0bpd65e6f36c8a8ca76@mail.gmail.com>

On Tue, Feb 19, 2008 at 2:27 AM, John Absher <john at absherneurology.com> wrote:
>  4 subjects, each had baseline CBF PET scans x 2, then they had
>  low-blood-pressure CBF PET scans x 2.
>
>  I have run the SPM2 analysis, but I also wanted to look at the ROIs.  I have
>  data for 115 ROIS, for each of the 4 PET scans obtained for each of the 4
>  subjects.

Are these 115 ROI's the same for each subject?  ie: did you draw them
or are they obtained by some automatic method?

>  What is the best statistic and correction method to use for evaluating the
>  significance of the regional changes in CBF when baseline measures are
>  compared to low-BP measures?

Well if understand you would have 115 mean values of CBF for each
"experiment". You would then I presume average the results of each of
the baseline and low-blood-flow images at which stage you would have
115 difference measures?

You would then have 115 difference across 4 subjects so at this stage
I presume you just need to discriminate which of them is more/most
predictive of the baseline vs low-blood-flow condition.

Do I have it right? :)  I guess the question of which stats would
depend on what you want out of this.  Do you want to know which ROI is
the best or where in each ROI is the best?  The former means a simple
stats analysis and the latter would get a tad more complicated (and i
suspect underpowered with only 4 subjects).


-- 
Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia +61 (402) 700 883

From a.janke at gmail.com  Fri Feb 22 07:07:14 2008
From: a.janke at gmail.com (Andrew Janke)
Date: Fri, 22 Feb 2008 23:07:14 +1100
Subject: [MINC-users] RMINC v0.4
In-Reply-To: <527B3E19-F16C-4744-B167-330F880FE46B@bic.mni.mcgill.ca>
References: <9f345c5b330a56021bfa067eabee0f4b@bic.mni.mcgill.ca>
	<e758a6650802131916u1c5af043k5a800ce5358622b6@mail.gmail.com>
	<527B3E19-F16C-4744-B167-330F880FE46B@bic.mni.mcgill.ca>
Message-ID: <d747ed50802220407lac3edfdjf4531a22bcb3b01e@mail.gmail.com>

>  * integration with debian/ubuntu packaging. Andrew liked this reason
>  in particular, given that debian packages appear to be our most
>  reliable binary packaging system at the moment.

I second (myself) on this one...

Launchpad is also great as it allows changes to be pushed upstream
also.  There is also the advantage of having packages participate in
nightly builds once they become part of Ubuntu/debian. I suspect
google code may have this but don't know.

Still these reasons really only make sense for the core packages.
Still I suspect that this decision may be out of our hands and we (the
royal ones) may in fact have to ask the McGill IP types if indeed we
are allowed to migrate "McGill" code ofsite.

Given that I am now back in Oz, I suspect that I cannot really
approach such people in McGill anymore. ;(

Thoughts?  or am I being overly cautious?

-- 
Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia +61 (402) 700 883

From jason at bic.mni.mcgill.ca  Fri Feb 22 08:32:55 2008
From: jason at bic.mni.mcgill.ca (Jason Lerch)
Date: Fri, 22 Feb 2008 08:32:55 -0500
Subject: [MINC-users] RMINC v0.4
In-Reply-To: <d747ed50802220407lac3edfdjf4531a22bcb3b01e@mail.gmail.com>
References: <9f345c5b330a56021bfa067eabee0f4b@bic.mni.mcgill.ca>
	<e758a6650802131916u1c5af043k5a800ce5358622b6@mail.gmail.com>
	<527B3E19-F16C-4744-B167-330F880FE46B@bic.mni.mcgill.ca>
	<d747ed50802220407lac3edfdjf4531a22bcb3b01e@mail.gmail.com>
Message-ID: <42897C00-8A80-4A24-A5CB-582FD36E4043@bic.mni.mcgill.ca>


>
> Still these reasons really only make sense for the core packages.
> Still I suspect that this decision may be out of our hands and we (the
> royal ones) may in fact have to ask the McGill IP types if indeed we
> are allowed to migrate "McGill" code ofsite.
>

If that is really an issue then there is an easy solution: launchpad  
can be used with code hosted anywhere publicly accessible, as long as  
the code is managed by the bazaar version control system. So it'd be  
quite easy to keep the code at www.bic.mni.mcgill.ca somewhere but  
still register it with launchpad in order to get the various benefits  
described above (and alternate branches created by non-mcgill folks  
can still be hosted directly at launchpad and be registered with the  
project.

> Given that I am now back in Oz, I suspect that I cannot really
> approach such people in McGill anymore. ;(
>
> Thoughts?  or am I being overly cautious?
>
> -- 
> Andrew Janke (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Canberra->Australia +61 (402) 700 883
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users


From bouffard at bic.mni.mcgill.ca  Fri Feb 22 10:27:25 2008
From: bouffard at bic.mni.mcgill.ca (Marc BOUFFARD)
Date: Fri, 22 Feb 2008 10:27:25 -0500
Subject: [MINC-users] ana2mnc
Message-ID: <Pine.SGI.4.58.0802221025100.18440910@yorick.bic.mni.mcgill.ca>

Hello,

is there another way than ana2mnc to convert analyse to mnc

when using ana2mnc file.hdr file.mnc

I get the following error:

Unknown data type: 512

Thank you

From claude at bic.mni.mcgill.ca  Fri Feb 22 10:30:42 2008
From: claude at bic.mni.mcgill.ca (Claude LEPAGE)
Date: Fri, 22 Feb 2008 10:30:42 -0500 (EST)
Subject: [MINC-users] ana2mnc
Message-ID: <200802221530.m1MFUgNb18466399@yorick.bic.mni.mcgill.ca>

> Hello,
> 
> is there another way than ana2mnc to convert analyse to mnc
> 
> when using ana2mnc file.hdr file.mnc

Yep. Try nii2mnc.

If the problem persists, let us know.

Claude

From a.janke at gmail.com  Mon Feb 25 15:14:48 2008
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 26 Feb 2008 07:14:48 +1100
Subject: [MINC-users] MINC 2.0.15
Message-ID: <d747ed50802251214hcd712dn151bc218356ddef9@mail.gmail.com>

Hi all,

After a lot of work by many MINC 2.0.15 is now ready for release. For
now it is only
in source form. Binary packages will follow shortly.

Get it here:

   http://packages.bic.mni.mcgill.ca/tgz/minc-2.0.15.tar.gz

The NEWS file summarises the changes as follows:

                New in Release 2.0.15
        ---------------------
* MINC2 is now built by default (or disabled with --diable-minc2).
* Began to aggregate and update all docs for a clean(er) 2.1 release
* Added cubic interpoation in mincresample for x-y slices
* Fixed a seg-fault with null history strings
* Changed all global variables to static to avoid linking problems
   with other libraries (eg: libz)
* new version of mincedit/mincheader in sh instead of csh
* Many fixes to remove compile warnings
* removed all rcsid's in files given that we have a -version argument
* Added preservation of "patient name" in nii2mnc (where patient name
   is the descriptor field in a nifti/analyze file)
* xfmconcat now records history in the output file
* removed all fortran build bits. This code was both out of date and
   not ever built
* removed get_image_offset as with a MINC2 file this would not work
   as it was it wouldn't work that well with MINC1 let along MINC2
* changed --enable-minc2 to --disable-minc2 in configure.ac
   (come what may....)

Take special note that MINC2 (with HDF5 support) is now built by default.


-- 
Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883