From a.janke at gmail.com  Wed Jan 29 00:25:05 2014
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 29 Jan 2014 15:25:05 +1000
Subject: [MINC-users] BIC Objects and Python
In-Reply-To: <CABApf9EacDjhqgQvofXty2003KcktugeEwtxxApCzci53Ndmdw@mail.gmail.com>
References: <CABApf9EacDjhqgQvofXty2003KcktugeEwtxxApCzci53Ndmdw@mail.gmail.com>
Message-ID: <CAG0CB22LoDuw2WkBJM8Ed1Xi1EtT4pEAbwzY4nta0+WbcnUbig@mail.gmail.com>

Hi Andrew,

On 1 January 2014 00:56, Andrew Wood <andrew at biospective.com> wrote:
> I was wondering if anyone has written something yet that can read/write BIC
> object files from Python.

Not that I am aware of and I don't see any other replies. If anyone
has it's probably something that Jason Lerch would know about.

ta

a

From jason at mouseimaging.ca  Wed Jan 29 06:51:19 2014
From: jason at mouseimaging.ca (Jason Lerch)
Date: Wed, 29 Jan 2014 06:51:19 -0500
Subject: [MINC-users] BIC Objects and Python
In-Reply-To: <CAG0CB22LoDuw2WkBJM8Ed1Xi1EtT4pEAbwzY4nta0+WbcnUbig@mail.gmail.com>
References: <CABApf9EacDjhqgQvofXty2003KcktugeEwtxxApCzci53Ndmdw@mail.gmail.com>
	<CAG0CB22LoDuw2WkBJM8Ed1Xi1EtT4pEAbwzY4nta0+WbcnUbig@mail.gmail.com>
Message-ID: <4D9CE990-6427-4582-9B43-F3636600B262@mouseimaging.ca>

Who, me? Sadly, no - something I would love to see, but don't think exists. 

Jason

> On Jan 29, 2014, at 12:25 AM, Andrew Janke <a.janke at gmail.com> wrote:
> 
> Hi Andrew,
> 
>> On 1 January 2014 00:56, Andrew Wood <andrew at biospective.com> wrote:
>> I was wondering if anyone has written something yet that can read/write BIC
>> object files from Python.
> 
> Not that I am aware of and I don't see any other replies. If anyone
> has it's probably something that Jason Lerch would know about.
> 
> ta
> 
> a
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From jon at pipitone.ca  Wed Jan 29 08:25:04 2014
From: jon at pipitone.ca (Jon Pipitone)
Date: Wed, 29 Jan 2014 08:25:04 -0500
Subject: [MINC-users] BIC Objects and Python
In-Reply-To: <4D9CE990-6427-4582-9B43-F3636600B262@mouseimaging.ca>
References: <CABApf9EacDjhqgQvofXty2003KcktugeEwtxxApCzci53Ndmdw@mail.gmail.com>
	<CAG0CB22LoDuw2WkBJM8Ed1Xi1EtT4pEAbwzY4nta0+WbcnUbig@mail.gmail.com>
	<4D9CE990-6427-4582-9B43-F3636600B262@mouseimaging.ca>
Message-ID: <20140129132504.GA2739@kensho.slice>

I once wrote a really hacky script to convert surfaces to the STL
format: 
   https://gist.github.com/pipitone/8687804

This was just something I reverse engineered in order to play with 3D
printing, but I too would love to see something more properly built.

Is there a spec for the format? A quick search turns up this: 
www.bic.mni.mcgill.ca/users/mishkin/mni_obj_format.pdf

Jon.



On 01/29, Jason Lerch wrote:
> Who, me? Sadly, no - something I would love to see, but don't think exists. 
> 
> Jason
> 
> > On Jan 29, 2014, at 12:25 AM, Andrew Janke <a.janke at gmail.com> wrote:
> > 
> > Hi Andrew,
> > 
> >> On 1 January 2014 00:56, Andrew Wood <andrew at biospective.com> wrote:
> >> I was wondering if anyone has written something yet that can read/write BIC
> >> object files from Python.
> > 
> > Not that I am aware of and I don't see any other replies. If anyone
> > has it's probably something that Jason Lerch would know about.
> > 
> > ta
> > 
> > a
> > _______________________________________________
> > 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 eskild at gmail.com  Wed Jan 29 08:37:05 2014
From: eskild at gmail.com (Simon Eskildsen)
Date: Wed, 29 Jan 2014 14:37:05 +0100
Subject: [MINC-users] BIC Objects and Python
In-Reply-To: <20140129132504.GA2739@kensho.slice>
References: <CABApf9EacDjhqgQvofXty2003KcktugeEwtxxApCzci53Ndmdw@mail.gmail.com>
	<CAG0CB22LoDuw2WkBJM8Ed1Xi1EtT4pEAbwzY4nta0+WbcnUbig@mail.gmail.com>
	<4D9CE990-6427-4582-9B43-F3636600B262@mouseimaging.ca>
	<20140129132504.GA2739@kensho.slice>
Message-ID: <CAD3v435TfoXii37_nk10KMYj3PCskvrb=x4QuuqOWSFscFQ+tg@mail.gmail.com>

There used to be a wiki page on the subject at the BIC here:
http://wiki.bic.mni.mcgill.ca/index.php/ObjectFiles
However, I'm not sure whether this moved "inside the walls" or completely
disappeared.

Simon


On Wed, Jan 29, 2014 at 2:25 PM, Jon Pipitone <jon at pipitone.ca> wrote:

> I once wrote a really hacky script to convert surfaces to the STL
> format:
>    https://gist.github.com/pipitone/8687804
>
> This was just something I reverse engineered in order to play with 3D
> printing, but I too would love to see something more properly built.
>
> Is there a spec for the format? A quick search turns up this:
> www.bic.mni.mcgill.ca/users/mishkin/mni_obj_format.pdf
>
> Jon.
>
>
>
> On 01/29, Jason Lerch wrote:
> > Who, me? Sadly, no - something I would love to see, but don't think
> exists.
> >
> > Jason
> >
> > > On Jan 29, 2014, at 12:25 AM, Andrew Janke <a.janke at gmail.com> wrote:
> > >
> > > Hi Andrew,
> > >
> > >> On 1 January 2014 00:56, Andrew Wood <andrew at biospective.com> wrote:
> > >> I was wondering if anyone has written something yet that can
> read/write BIC
> > >> object files from Python.
> > >
> > > Not that I am aware of and I don't see any other replies. If anyone
> > > has it's probably something that Jason Lerch would know about.
> > >
> > > ta
> > >
> > > a
> > > _______________________________________________
> > > 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
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From sylvain at bic.mni.mcgill.ca  Wed Jan 29 09:05:22 2014
From: sylvain at bic.mni.mcgill.ca (Sylvain Milot)
Date: Wed, 29 Jan 2014 09:05:22 -0500 (EST)
Subject: [MINC-users] BIC Objects and Python
In-Reply-To: <CAD3v435TfoXii37_nk10KMYj3PCskvrb=x4QuuqOWSFscFQ+tg@mail.gmail.com>
References: <CABApf9EacDjhqgQvofXty2003KcktugeEwtxxApCzci53Ndmdw@mail.gmail.com>
	<CAG0CB22LoDuw2WkBJM8Ed1Xi1EtT4pEAbwzY4nta0+WbcnUbig@mail.gmail.com>
	<4D9CE990-6427-4582-9B43-F3636600B262@mouseimaging.ca>
	<20140129132504.GA2739@kensho.slice>
	<CAD3v435TfoXii37_nk10KMYj3PCskvrb=x4QuuqOWSFscFQ+tg@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.1401290902550.29468@nestor.bic.mni.mcgill.ca>


This was part of the old wiki and you should find it here:
http://wikiobs.bic.mni.mcgill.ca/index.php/ObjectFiles

this will only be available inside the BIC network.

Sylvain

On Wed, 29 Jan 2014, Simon Eskildsen wrote:

> There used to be a wiki page on the subject at the BIC here:
> http://wiki.bic.mni.mcgill.ca/index.php/ObjectFiles
> However, I'm not sure whether this moved "inside the walls" or completely
> disappeared.
>
> Simon
>
>
> On Wed, Jan 29, 2014 at 2:25 PM, Jon Pipitone <jon at pipitone.ca> wrote:
>
>> I once wrote a really hacky script to convert surfaces to the STL
>> format:
>>    https://gist.github.com/pipitone/8687804
>>
>> This was just something I reverse engineered in order to play with 3D
>> printing, but I too would love to see something more properly built.
>>
>> Is there a spec for the format? A quick search turns up this:
>> www.bic.mni.mcgill.ca/users/mishkin/mni_obj_format.pdf
>>
>> Jon.
>>
>>
>>
>> On 01/29, Jason Lerch wrote:
>>> Who, me? Sadly, no - something I would love to see, but don't think
>> exists.
>>>
>>> Jason
>>>
>>>> On Jan 29, 2014, at 12:25 AM, Andrew Janke <a.janke at gmail.com> wrote:
>>>>
>>>> Hi Andrew,
>>>>
>>>>> On 1 January 2014 00:56, Andrew Wood <andrew at biospective.com> wrote:
>>>>> I was wondering if anyone has written something yet that can
>> read/write BIC
>>>>> object files from Python.
>>>>
>>>> Not that I am aware of and I don't see any other replies. If anyone
>>>> has it's probably something that Jason Lerch would know about.
>>>>
>>>> ta
>>>>
>>>> a
>>>> _______________________________________________
>>>> 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
>> _______________________________________________
>> 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 eskild at gmail.com  Wed Jan 29 09:09:13 2014
From: eskild at gmail.com (Simon Eskildsen)
Date: Wed, 29 Jan 2014 15:09:13 +0100
Subject: [MINC-users] BIC Objects and Python
In-Reply-To: <Pine.LNX.4.64.1401290902550.29468@nestor.bic.mni.mcgill.ca>
References: <CABApf9EacDjhqgQvofXty2003KcktugeEwtxxApCzci53Ndmdw@mail.gmail.com>
	<CAG0CB22LoDuw2WkBJM8Ed1Xi1EtT4pEAbwzY4nta0+WbcnUbig@mail.gmail.com>
	<4D9CE990-6427-4582-9B43-F3636600B262@mouseimaging.ca>
	<20140129132504.GA2739@kensho.slice>
	<CAD3v435TfoXii37_nk10KMYj3PCskvrb=x4QuuqOWSFscFQ+tg@mail.gmail.com>
	<Pine.LNX.4.64.1401290902550.29468@nestor.bic.mni.mcgill.ca>
Message-ID: <CAD3v435B2hH2xqY5Mw2S0tAbqZdV1=kwbe4vmfmQW8P+=pi3RA@mail.gmail.com>

Yes, that's what I thought. Any reason for restricting public access?

Simon


On Wed, Jan 29, 2014 at 3:05 PM, Sylvain Milot <sylvain at bic.mni.mcgill.ca>wrote:

>
> This was part of the old wiki and you should find it here:
> http://wikiobs.bic.mni.mcgill.ca/index.php/ObjectFiles
>
> this will only be available inside the BIC network.
>
> Sylvain
>
>
> On Wed, 29 Jan 2014, Simon Eskildsen wrote:
>
>  There used to be a wiki page on the subject at the BIC here:
>> http://wiki.bic.mni.mcgill.ca/index.php/ObjectFiles
>> However, I'm not sure whether this moved "inside the walls" or completely
>> disappeared.
>>
>> Simon
>>
>>
>> On Wed, Jan 29, 2014 at 2:25 PM, Jon Pipitone <jon at pipitone.ca> wrote:
>>
>>  I once wrote a really hacky script to convert surfaces to the STL
>>> format:
>>>    https://gist.github.com/pipitone/8687804
>>>
>>> This was just something I reverse engineered in order to play with 3D
>>> printing, but I too would love to see something more properly built.
>>>
>>> Is there a spec for the format? A quick search turns up this:
>>> www.bic.mni.mcgill.ca/users/mishkin/mni_obj_format.pdf
>>>
>>> Jon.
>>>
>>>
>>>
>>> On 01/29, Jason Lerch wrote:
>>>
>>>> Who, me? Sadly, no - something I would love to see, but don't think
>>>>
>>> exists.
>>>
>>>>
>>>> Jason
>>>>
>>>>  On Jan 29, 2014, at 12:25 AM, Andrew Janke <a.janke at gmail.com> wrote:
>>>>>
>>>>> Hi Andrew,
>>>>>
>>>>>  On 1 January 2014 00:56, Andrew Wood <andrew at biospective.com> wrote:
>>>>>> I was wondering if anyone has written something yet that can
>>>>>>
>>>>> read/write BIC
>>>
>>>> object files from Python.
>>>>>>
>>>>>
>>>>> Not that I am aware of and I don't see any other replies. If anyone
>>>>> has it's probably something that Jason Lerch would know about.
>>>>>
>>>>> ta
>>>>>
>>>>> a
>>>>> _______________________________________________
>>>>> 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
>>>>
>>> _______________________________________________
>>> 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
>>
>>  _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From sylvain at bic.mni.mcgill.ca  Wed Jan 29 09:12:39 2014
From: sylvain at bic.mni.mcgill.ca (Sylvain Milot)
Date: Wed, 29 Jan 2014 09:12:39 -0500 (EST)
Subject: [MINC-users] BIC Objects and Python
In-Reply-To: <CAD3v435B2hH2xqY5Mw2S0tAbqZdV1=kwbe4vmfmQW8P+=pi3RA@mail.gmail.com>
References: <CABApf9EacDjhqgQvofXty2003KcktugeEwtxxApCzci53Ndmdw@mail.gmail.com>
	<CAG0CB22LoDuw2WkBJM8Ed1Xi1EtT4pEAbwzY4nta0+WbcnUbig@mail.gmail.com>
	<4D9CE990-6427-4582-9B43-F3636600B262@mouseimaging.ca>
	<20140129132504.GA2739@kensho.slice>
	<CAD3v435TfoXii37_nk10KMYj3PCskvrb=x4QuuqOWSFscFQ+tg@mail.gmail.com>
	<Pine.LNX.4.64.1401290902550.29468@nestor.bic.mni.mcgill.ca>
	<CAD3v435B2hH2xqY5Mw2S0tAbqZdV1=kwbe4vmfmQW8P+=pi3RA@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.1401290910230.29468@nestor.bic.mni.mcgill.ca>


it is old and should be moved to the new platform.

Sylvain

On Wed, 29 Jan 2014, Simon Eskildsen wrote:

> Yes, that's what I thought. Any reason for restricting public access?
>
> Simon
>
>
> On Wed, Jan 29, 2014 at 3:05 PM, Sylvain Milot <sylvain at bic.mni.mcgill.ca>wrote:
>
>>
>> This was part of the old wiki and you should find it here:
>> http://wikiobs.bic.mni.mcgill.ca/index.php/ObjectFiles
>>
>> this will only be available inside the BIC network.
>>
>> Sylvain
>>
>>
>> On Wed, 29 Jan 2014, Simon Eskildsen wrote:
>>
>>  There used to be a wiki page on the subject at the BIC here:
>>> http://wiki.bic.mni.mcgill.ca/index.php/ObjectFiles
>>> However, I'm not sure whether this moved "inside the walls" or completely
>>> disappeared.
>>>
>>> Simon
>>>
>>>
>>> On Wed, Jan 29, 2014 at 2:25 PM, Jon Pipitone <jon at pipitone.ca> wrote:
>>>
>>>  I once wrote a really hacky script to convert surfaces to the STL
>>>> format:
>>>>    https://gist.github.com/pipitone/8687804
>>>>
>>>> This was just something I reverse engineered in order to play with 3D
>>>> printing, but I too would love to see something more properly built.
>>>>
>>>> Is there a spec for the format? A quick search turns up this:
>>>> www.bic.mni.mcgill.ca/users/mishkin/mni_obj_format.pdf
>>>>
>>>> Jon.
>>>>
>>>>
>>>>
>>>> On 01/29, Jason Lerch wrote:
>>>>
>>>>> Who, me? Sadly, no - something I would love to see, but don't think
>>>>>
>>>> exists.
>>>>
>>>>>
>>>>> Jason
>>>>>
>>>>>  On Jan 29, 2014, at 12:25 AM, Andrew Janke <a.janke at gmail.com> wrote:
>>>>>>
>>>>>> Hi Andrew,
>>>>>>
>>>>>>  On 1 January 2014 00:56, Andrew Wood <andrew at biospective.com> wrote:
>>>>>>> I was wondering if anyone has written something yet that can
>>>>>>>
>>>>>> read/write BIC
>>>>
>>>>> object files from Python.
>>>>>>>
>>>>>>
>>>>>> Not that I am aware of and I don't see any other replies. If anyone
>>>>>> has it's probably something that Jason Lerch would know about.
>>>>>>
>>>>>> ta
>>>>>>
>>>>>> a
>>>>>> _______________________________________________
>>>>>> 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
>>>>>
>>>> _______________________________________________
>>>> 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
>>>
>>>  _______________________________________________
>> 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
>


---

     If you have questions or requests specific to the B.I.C, please get in touch with
                          <bicadmin at bic.mni.mcgill.ca>

     Our ssh login server is login.bic.mni.mcgill.ca
     ssh RSA key fingerprint is 3a:e3:32:f3:2e:7f:cf:94:1c:47:50:4f:c2:b5:93:9b

---
Sylvain Milot (sylvain at bic.mni.mcgill.ca)
               (sylvain.milot at mcgill.ca)
Brain Imaging Centre
Montreal Neurological Institute
3801 University Street
Webster 2B, Room 206
Montreal, Qc., Canada, H3A 2B4
Phone  : (514) 398-4965, Fax: 398-8948
Mobile : (514) 712-1768
Office : 527 Av Des Pins O., Room 104
          Montreal, Qc., H2W 1S4

From jon at pipitone.ca  Wed Jan 29 09:18:59 2014
From: jon at pipitone.ca (Jon Pipitone)
Date: Wed, 29 Jan 2014 09:18:59 -0500
Subject: [MINC-users] BIC Objects and Python
In-Reply-To: <Pine.LNX.4.64.1401290910230.29468@nestor.bic.mni.mcgill.ca>
References: <CABApf9EacDjhqgQvofXty2003KcktugeEwtxxApCzci53Ndmdw@mail.gmail.com>
	<CAG0CB22LoDuw2WkBJM8Ed1Xi1EtT4pEAbwzY4nta0+WbcnUbig@mail.gmail.com>
	<4D9CE990-6427-4582-9B43-F3636600B262@mouseimaging.ca>
	<20140129132504.GA2739@kensho.slice>
	<CAD3v435TfoXii37_nk10KMYj3PCskvrb=x4QuuqOWSFscFQ+tg@mail.gmail.com>
	<Pine.LNX.4.64.1401290902550.29468@nestor.bic.mni.mcgill.ca>
	<CAD3v435B2hH2xqY5Mw2S0tAbqZdV1=kwbe4vmfmQW8P+=pi3RA@mail.gmail.com>
	<Pine.LNX.4.64.1401290910230.29468@nestor.bic.mni.mcgill.ca>
Message-ID: <20140129141859.GA3146@kensho.slice>

Perhaps someone could either post the content to the list, or add it to
the Wikibook? 

Jon.

On 01/29, Sylvain Milot wrote:
> 
> it is old and should be moved to the new platform.
> 
> Sylvain
> 
> On Wed, 29 Jan 2014, Simon Eskildsen wrote:
> 
> >Yes, that's what I thought. Any reason for restricting public access?
> >
> >Simon
> >
> >
> >On Wed, Jan 29, 2014 at 3:05 PM, Sylvain Milot <sylvain at bic.mni.mcgill.ca>wrote:
> >
> >>
> >>This was part of the old wiki and you should find it here:
> >>http://wikiobs.bic.mni.mcgill.ca/index.php/ObjectFiles
> >>
> >>this will only be available inside the BIC network.
> >>
> >>Sylvain

From sylvain at bic.mni.mcgill.ca  Wed Jan 29 11:21:16 2014
From: sylvain at bic.mni.mcgill.ca (Sylvain Milot)
Date: Wed, 29 Jan 2014 11:21:16 -0500 (EST)
Subject: [MINC-users] BIC Objects and Python
In-Reply-To: <20140129141859.GA3146@kensho.slice>
References: <CABApf9EacDjhqgQvofXty2003KcktugeEwtxxApCzci53Ndmdw@mail.gmail.com>
	<CAG0CB22LoDuw2WkBJM8Ed1Xi1EtT4pEAbwzY4nta0+WbcnUbig@mail.gmail.com>
	<4D9CE990-6427-4582-9B43-F3636600B262@mouseimaging.ca>
	<20140129132504.GA2739@kensho.slice>
	<CAD3v435TfoXii37_nk10KMYj3PCskvrb=x4QuuqOWSFscFQ+tg@mail.gmail.com>
	<Pine.LNX.4.64.1401290902550.29468@nestor.bic.mni.mcgill.ca>
	<CAD3v435B2hH2xqY5Mw2S0tAbqZdV1=kwbe4vmfmQW8P+=pi3RA@mail.gmail.com>
	<Pine.LNX.4.64.1401290910230.29468@nestor.bic.mni.mcgill.ca>
	<20140129141859.GA3146@kensho.slice>
Message-ID: <Pine.LNX.4.64.1401291120440.29468@nestor.bic.mni.mcgill.ca>


you will find a section at http://www.bic.mni.mcgill.ca/Services/HowTo

Sylvain

On Wed, 29 Jan 2014, Jon Pipitone wrote:

> Perhaps someone could either post the content to the list, or add it to
> the Wikibook?
>
> Jon.
>
> On 01/29, Sylvain Milot wrote:
>>
>> it is old and should be moved to the new platform.
>>
>> Sylvain
>>
>> On Wed, 29 Jan 2014, Simon Eskildsen wrote:
>>
>>> Yes, that's what I thought. Any reason for restricting public access?
>>>
>>> Simon
>>>
>>>
>>> On Wed, Jan 29, 2014 at 3:05 PM, Sylvain Milot <sylvain at bic.mni.mcgill.ca>wrote:
>>>
>>>>
>>>> This was part of the old wiki and you should find it here:
>>>> http://wikiobs.bic.mni.mcgill.ca/index.php/ObjectFiles
>>>>
>>>> this will only be available inside the BIC network.
>>>>
>>>> Sylvain
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From zijdenbos at gmail.com  Fri Jan 31 17:10:02 2014
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Fri, 31 Jan 2014 17:10:02 -0500
Subject: [MINC-users] minctracc/masking bug?
In-Reply-To: <CABEEk17hsvZYETWo5+8FsVG4ifQHXYmOTYAxuG9B4WwpXMfcAg@mail.gmail.com>
References: <CABEEk17HNT+vaaMFevinaYXLp_VZbXn=jsdjzJq2wavLD9a85g@mail.gmail.com>
	<201305101800.r4AI0pIH014948@agrippa.bic.mni.mcgill.ca>
	<CABEEk168XGLodvKH6NCPT9WiA+V-Tvi9t8-gQgdkOeRNpmGQmA@mail.gmail.com>
	<CAMCwi7OGT1takr2ieMvSH+zHnVUXOL5b7AYzZw=CJwoexR0_Cw@mail.gmail.com>
	<CABEEk16M3sjag783x8JPbOxWUBVkG6aiTXS2d909rRxCWXTHBA@mail.gmail.com>
	<CABEEk17hsvZYETWo5+8FsVG4ifQHXYmOTYAxuG9B4WwpXMfcAg@mail.gmail.com>
Message-ID: <CABEEk15+AAeaOGhVDgMtDMKBVbOeZPxnZvz-dk0cY8bNsbBmew@mail.gmail.com>

Hello all,

Reviving an issue I raised last year, that I believe we have now fixed
(thanks to Fran?ois H?bert and Andrew Wood!). To summarize, for a long time
we've been plagued by minctracc's tendency to favor positive directions
along the parameter space dimensions. This affects both linear- and
non-linear registration; for the linear registration this results in biases
with respect to orientation; for the non-linear, this results in a tendency
to 'inflate' towards positive directions (as a result of which, by the way,
I believe that any studies of brain asymmetry using minctracc, or any kind
of sidedness in fact, are suspect).

The cause turned out to be in the initialization of the simplex/amoeba
optimization, which always initializes itself towards the positive end of
the parameter axes, at line 270 of
amoeba.c<https://github.com/BIC-MNI/mni_autoreg/blob/master/minctracc/Optimize/amoeba.c>.
This results in an inherent bias of the optimization in those directions.
We have fixed this by also evaluating the mirrored (negative) starting
position along each axis, resulting in a directionally unbiased amoeba
initialization.

To illustrate the effect and fix, I generate 3 animated gifs as examples.
Each of these flip between 'old' and 'new' (make sure the viewer you use
speaks animated gif):

1. human_average_lin<https://www.dropbox.com/s/hn45jqmisby9h8v/asym_avg.gif>:
linear average of ~100 scans. You will see the tendency of the 'old'
towards more positive rotations and translations

2. human_single_nonlin<https://www.dropbox.com/s/bidmbzmjt77jm2l/verify.gif>:
single subject; you will see the asymmetric 'blowout' of the resampled
image.

3. mouse_single_nonlin<https://www.dropbox.com/s/54ae54wh4zex4v1/verify_mouse.gif>:
single mouse. In this case, both the source- and target images are
symmetric about x=0, so one would expect a symmetric deformation field as a
result. The bottom row shows the deformation magnitude of the transform,
clearly showing its asymmetry with the old minctracc, versus the symmetric
def with the patched amoeba.c.

Andrew Wood will submit the updated code next week.

Have a good weekend!

-- Alex


On Wed, May 22, 2013 at 12:11 AM, Alex Zijdenbos <zijdenbos at gmail.com>wrote:

> OK, by popular demand, I generated some data and wrote a simple script
> that illustrates the issue discussed here. Although I have already
> seen that masking can have a drastic impact on the deformation
> asymmetry, this example keeps it simple by not using masks, nor
> blurring; it uses a simple and single minctracc call, with 1
> iteration.
>
> Here is the tarball:
>
>    https://dl.dropboxusercontent.com/u/5709165/MINC/SymTestDist.tar.gz
>
> To run the experiment:
>
>    tar zxvf /home/alex/pchome/Scratch/SymTestDist.tar.gz
>    cd SymTestDist/
>    ./run_sym_test.pl -tmpdir tmp image.mnc model.mnc resdiff.mnc
> defdiffmag.mnc | tee sym_test.log
>
> This will:
>
> - register image.mnc (asymmetric) to model.mnc (symmetric)
> - register them again after flipping both image.mnc and model.mnc about x=0
> - flip the flipped resampled image and the flipped deformation field back
> - generate the subtraction of the two resampled files (resdiff.mnc)
> - generate the magnitude of the difference between the two deformation
> fields (defdiffmag.mnc).
>
> In an ideal situation, both output files would be 0; any non-zero
> values in these two output files indicate a methodological asymmetry
> in the deformation field that minctracc generates. You can in fact
> obtain "perfect" (0, barring some slice scaling) output by registering
> model.mnc to itself. However, as another test, use model_0.99.mnc as
> the source image; this is model.mnc shrunk a small amount by scaling
> it by 0.99 in all dimensions. You will see that the asymmetric
> behaviour immediately shows up even in this case.
>
> -- A
>
>
>
> On Tue, May 21, 2013 at 12:05 PM, Alex Zijdenbos <zijdenbos at gmail.com>
> wrote:
> > Hi Vlad,
> >
> > I simply flipped the grid file itself (resample it with $flip,
> > essentially), so without going through xfmconcat and xfm2def. Just to
> > be sure I just tested this on one case, and the results of your
> > process and simply flipping the grid file are identical.
> >
> > As for the asymmetry, I will pursue this further following Andrew's
> > suggestions as well; I'll try to narrow it down to something simple
> > that I can easily share.
> >
> > -- A
> >
> > On Tue, May 21, 2013 at 10:28 AM, Vladimir S. FONOV
> > <vladimir.fonov at gmail.com> wrote:
> >> What is the procedure that you are using for flipping the grid file ?
> >>
> >> The way how I am doing it in my symmetric model building script (
> >> https://github.com/vfonov/build_average_model )  :
> >>
> >> nlfit_s $input $model $tempdir/left_nl.xfm -source_mask $input_mask
> >> -target_mask $model_mask -level $level
> >>
> >> nlfit_s $input_flip $model $tempdir/right_nl.xfm -source_mask
> >> $input_flip_mask -target_mask $model_mask \
> >>      -level $level -work_dir $tempdir
> >>
> >> xfm_normalize.pl $tempdir/left_nl.xfm $tempdir/output_left.xfm -like
> >> $model --step $level
> >>
> >> xfmconcat $flip $tempdir/right_nl.xfm $flip $tempdir/right_nl_flip.xfm
> >>
> >> #make nonlinear only
> >> xfm_normalize.pl $tempdir/right_nl_flip.xfm
> >> $tempdir/output_right_flip.xfm -like $model --step $level
> >>
> >> #average left and right flipped
> >> xfmavg $tempdir/output_left.xfm $tempdir/output_right_flip.xfm $output
> >>
> >> On Tue, May 21, 2013 at 12:07 AM, Alex Zijdenbos <zijdenbos at gmail.com>
> wrote:
> >>> Thanks, Claude - looking at your suggestions (and at the minctracc
> >>> source code). In the mean time, I performed some phenomenological
> >>> experiments that I thought would be interesting to share. Here's what
> >>> I did:
> >>>
> >>> - take 100 subjects, already in linear template (stx) space
> >>> - register these with an nlfit*-like process, up to 4mm grid step
> >>> size, to a symmetric template+mask
> >>> - flip the subject image and its mask about x=0, repeat the
> registration
> >>> - flip the resampled image and the grid from the registration again
> about x=0
> >>> - calculate the magnitude of the difference between the 'normal' and
> >>> '2xflipped' grid (per subject)
> >>>
> >>> - average the 'normal' and '2xflipped' grid files across subjects
> >>> - calculate the magnitude of the difference between the average
> >>> 'normal' and average '2xflipped' grid files
> >>>
> >>> In the end, what I am left with is the asymmetry in the deformation
> >>> field(s) due solely to the registration process; if minctracc were
> >>> unbiased, these difference images would be 0. This image:
> >>>
> >>> https://dl.dropboxusercontent.com/u/5709165/def_diff_mag.jpeg
> >>>
> >>> shows the average of the non-linearly registered images over these 100
> >>> subjects; and the magnitude of the difference of the average
> >>> deformation estimated 'normally' and '2xflipped'. Note that the in
> >>> these population averages, the maximum deformation magnitude is 2.86;
> >>> in individual subjects, the max magnitude of the deformation
> >>> difference is typically in the 10-20 range. In other words, the
> >>> asymmetry in the estimated deformation field purely caused by the
> >>> methodology, can be as high as 20mm.
> >>>
> >>> I'd be very happy if somebody could run a similar experiment, if
> >>> anything on a single subject; just to confirm that I didn't do
> >>> anything fundamentally wrong somewhere (which would be great).
> >>>
> >>> -- A
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> On Fri, May 10, 2013 at 2:00 PM, Claude LEPAGE <
> claude at bic.mni.mcgill.ca> wrote:
> >>>> Alex,
> >>>>
> >>>>> So far the only explanation I can think of, is that the optimizer
> >>>>> follows a particular/fixed trajectory through the parameter space,
> >>>>> implicitly generating an "expansion force" in a particular direction
> >>>>> that can go unchecked given the right set of circumstances (a
> >>>>> particular mask being one of them). Anyways, still testing different
> >>>>> parameters, will report on what I find.
> >>>>
> >>>> Can you do only 1 iteration of minctracc? Is symmetry preserved?
> >>>> Try this 1 iteration with and without smoothing (set smoothing weight
> >>>> to zero). Still symmetric?
> >>>>
> >>>> Your suggestion above sounds like the result could be influenced by
> >>>> the order of the loops. This is a common mistake in numerical
> analysis.
> >>>> For example:
> >>>>    vec[i] = some_function( vec[i-1], vec[i], vec[i+1] );
> >>>> When you process vec[i+1], the value of its previous neighbour has
> >>>> changed, so running the loop forward/backward gives a different
> answer.
> >>>> You can check the code for something like this (good luck).
> >>>>
> >>>> Have you tried minctracc 0.99.3? Have you tried mincreshape to change
> >>>> the x,y,z ordering? I doubt this will have an impact on the results.
> >>>>
> >>>> Claude
> >>>>
> >>>> _______________________________________________
> >>>> 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
> >>
> >>
> >>
> >> --
> >> Best regards,
> >>
> >>  Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
> >> _______________________________________________
> >> MINC-users at bic.mni.mcgill.ca
> >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>
>