From vladimir.fonov at gmail.com  Mon Jul  3 14:12:57 2017
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Mon, 3 Jul 2017 14:12:57 -0400
Subject: [MINC-users] minc-toolkit new release 1.9.15 and 1.0.09
Message-ID: <6d8ce820-cc80-a8fa-e005-cc73d52a5d24@gmail.com>

Hello Everybody,

I finally put new minc-toolkit online, you can download it through 
http://bic-mni.github.io/

On the BIC system, it is installed in /ipl/quarantine/experimental/1.9.15

One important difference with old releases is that all the files from 
minc-toolkit-* packages are now installed in /opt/minc/1.XX.YY 
directory, but data files ( MNI models, Beast libraries , etc) are still 
installed in /opt/minc, this allows to have several versions of 
minc-toolkit to co-exist on the same system.

-- 
Best regards,

  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com

From andrew at biospective.com  Tue Jul 11 17:28:46 2017
From: andrew at biospective.com (Andrew Wood)
Date: Tue, 11 Jul 2017 17:28:46 -0400
Subject: [MINC-users] Visualizing a surface mask
Message-ID: <CABApf9ExUf_zvEaSch7RVsjZorR+WeptRsCWL-1F5v04LOc7Ew@mail.gmail.com>

Hi all,

I'm trying to visualize a surface atlas file (.txt) on a surface (.obj).
Does this functionality exist in Display?

Thanks,
Andrew

From claude at bic.mni.mcgill.ca  Tue Jul 11 17:37:36 2017
From: claude at bic.mni.mcgill.ca (Claude LEPAGE)
Date: Tue, 11 Jul 2017 17:37:36 -0400
Subject: [MINC-users] Visualizing a surface mask
In-Reply-To: <CABApf9ExUf_zvEaSch7RVsjZorR+WeptRsCWL-1F5v04LOc7Ew@mail.gmail.com>
Message-ID: <201707112137.v6BLbaGD007535@login1.bic.mni.mcgill.ca>


1) Use colour_object to import .txt into .obj. Load .obj in Display.

2) Use brainbrowser http://aces.github.io/bigbrain-surface-viewer/.

3) Use brain-view from Jason Lerch. 


>
> Hi all,
>
> I'm trying to visualize a surface atlas file (.txt) on a surface (.obj).
> Does this functionality exist in Display?
>
> Thanks,
> Andrew
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From bert at phalarope.com  Tue Jul 11 17:46:58 2017
From: bert at phalarope.com (Robert D. Vincent)
Date: Tue, 11 Jul 2017 17:46:58 -0400
Subject: [MINC-users] Visualizing a surface mask
In-Reply-To: <CABApf9ExUf_zvEaSch7RVsjZorR+WeptRsCWL-1F5v04LOc7Ew@mail.gmail.com>
References: <CABApf9ExUf_zvEaSch7RVsjZorR+WeptRsCWL-1F5v04LOc7Ew@mail.gmail.com>
Message-ID: <CAAd5DeToQjN68FcWhmrxz2Qd14B3gYQ==LT8RSJc=hVe=gbB+A@mail.gmail.com>

You can use the -vertex option to load vertex data directly into recent
versions of Display.

    -bert


On Jul 11, 2017 6:30 PM, "Andrew Wood" <andrew at biospective.com> wrote:

> Hi all,
>
> I'm trying to visualize a surface atlas file (.txt) on a surface (.obj).
> Does this functionality exist in Display?
>
> Thanks,
> Andrew
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From andrew at biospective.com  Mon Jul 17 14:24:33 2017
From: andrew at biospective.com (Andrew Wood)
Date: Mon, 17 Jul 2017 14:24:33 -0400
Subject: [MINC-users] Visualizing a surface mask
In-Reply-To: <CAAd5DeToQjN68FcWhmrxz2Qd14B3gYQ==LT8RSJc=hVe=gbB+A@mail.gmail.com>
References: <CABApf9ExUf_zvEaSch7RVsjZorR+WeptRsCWL-1F5v04LOc7Ew@mail.gmail.com>
	<CAAd5DeToQjN68FcWhmrxz2Qd14B3gYQ==LT8RSJc=hVe=gbB+A@mail.gmail.com>
Message-ID: <CABApf9EUuLmAFwc25DPjhrLgWyYBXKUFk4wqpRgffrKT+pkqDw@mail.gmail.com>

Hi Bert,

Is there way to save vertex colours back out to a .txt file?

Thanks,
Andrew

On Tue, Jul 11, 2017 at 5:46 PM, Robert D. Vincent <bert at phalarope.com>
wrote:

> You can use the -vertex option to load vertex data directly into recent
> versions of Display.
>
>     -bert
>
>
> On Jul 11, 2017 6:30 PM, "Andrew Wood" <andrew at biospective.com> wrote:
>
> > Hi all,
> >
> > I'm trying to visualize a surface atlas file (.txt) on a surface (.obj).
> > Does this functionality exist in Display?
> >
> > Thanks,
> > Andrew
> > _______________________________________________
> > 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 bert at phalarope.com  Mon Jul 17 20:09:50 2017
From: bert at phalarope.com (Robert D. Vincent)
Date: Mon, 17 Jul 2017 20:09:50 -0400
Subject: [MINC-users] Visualizing a surface mask
In-Reply-To: <CABApf9EUuLmAFwc25DPjhrLgWyYBXKUFk4wqpRgffrKT+pkqDw@mail.gmail.com>
References: <CABApf9ExUf_zvEaSch7RVsjZorR+WeptRsCWL-1F5v04LOc7Ew@mail.gmail.com>
	<CAAd5DeToQjN68FcWhmrxz2Qd14B3gYQ==LT8RSJc=hVe=gbB+A@mail.gmail.com>
	<CABApf9EUuLmAFwc25DPjhrLgWyYBXKUFk4wqpRgffrKT+pkqDw@mail.gmail.com>
Message-ID: <CAAd5DeRqkEgyHghL3P0mZZBoH781bd6CuMSHeiKBhq89w51GVw@mail.gmail.com>

Hi Andrew,

Not that I have implemented. You can save the colored obj file, but not the
separate txt file.

     -bert

On Mon, Jul 17, 2017 at 2:24 PM, Andrew Wood <andrew at biospective.com> wrote:

> Hi Bert,
>
> Is there way to save vertex colours back out to a .txt file?
>
> Thanks,
> Andrew
>
> On Tue, Jul 11, 2017 at 5:46 PM, Robert D. Vincent <bert at phalarope.com>
> wrote:
>
> > You can use the -vertex option to load vertex data directly into recent
> > versions of Display.
> >
> >     -bert
> >
> >
> > On Jul 11, 2017 6:30 PM, "Andrew Wood" <andrew at biospective.com> wrote:
> >
> > > Hi all,
> > >
> > > I'm trying to visualize a surface atlas file (.txt) on a surface
> (.obj).
> > > Does this functionality exist in Display?
> > >
> > > Thanks,
> > > Andrew
> > > _______________________________________________
> > > 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 redoute at cermep.fr  Wed Jul 19 09:34:42 2017
From: redoute at cermep.fr (=?UTF-8?B?SsOpcsO0bWUgUmVkb3V0w6k=?=)
Date: Wed, 19 Jul 2017 15:34:42 +0200
Subject: [MINC-users] dcm2mnc issue
Message-ID: <134957f4-e5b6-f659-6f0d-1e91958e5292@cermep.fr>

Dear All,

we are facing issues while converting dynamic PET data from DICOM to MINC.

For some studies, important header informations such as radionucleide, 
isotope half life.. are lost.

Furthermore, when we want to convert this mnc files into ECAT using 
minctoecat, singles counts are not available in the resulting ecat file .

This problem is not present for all studies from the same scanner 
(SIEMENS biograph mCT), some are working, others don't.

I can provide links to download test dataset if someone needs.

Thank you for your help

Jerome

-- 
==================================================================
J?r?me Redout?
Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1
CERMEP - Imagerie du vivant
59 Bd Pinel. 69677 Bron - FRANCE
tel : 33 (0)4 72 68 86 18 (bureau)
tel : 33 (0)4 72 68 86 00 (standard)
fax : 33 (0)4 72 68 86 10
==================================================================



From bert at phalarope.com  Wed Jul 19 10:28:51 2017
From: bert at phalarope.com (Robert D. Vincent)
Date: Wed, 19 Jul 2017 10:28:51 -0400
Subject: [MINC-users] dcm2mnc issue
In-Reply-To: <134957f4-e5b6-f659-6f0d-1e91958e5292@cermep.fr>
References: <134957f4-e5b6-f659-6f0d-1e91958e5292@cermep.fr>
Message-ID: <CAAd5DeRP=An4tZgAOigPSdPSq2MWAxCUes4YJO9DgjDULrF0eA@mail.gmail.com>

Hi Jerome,

Feel free to forward that to me and I'll try to take a look at it.

    -bert

On Wed, Jul 19, 2017 at 9:34 AM, J?r?me Redout? <redoute at cermep.fr> wrote:

> Dear All,
>
> we are facing issues while converting dynamic PET data from DICOM to MINC.
>
> For some studies, important header informations such as radionucleide,
> isotope half life.. are lost.
>
> Furthermore, when we want to convert this mnc files into ECAT using
> minctoecat, singles counts are not available in the resulting ecat file .
>
> This problem is not present for all studies from the same scanner (SIEMENS
> biograph mCT), some are working, others don't.
>
> I can provide links to download test dataset if someone needs.
>
> Thank you for your help
>
> Jerome
>
> --
> ==================================================================
> J?r?me Redout?
> Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1
> CERMEP - Imagerie du vivant
> 59 Bd Pinel. 69677 Bron - FRANCE
> tel : 33 (0)4 72 68 86 18 (bureau)
> tel : 33 (0)4 72 68 86 00 (standard)
> fax : 33 (0)4 72 68 86 10
> ==================================================================
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From ptcougopinto at gmail.com  Thu Jul 27 15:24:48 2017
From: ptcougopinto at gmail.com (Pedro)
Date: Thu, 27 Jul 2017 16:24:48 -0300
Subject: [MINC-users] Proper citation
Message-ID: <C2554A26-BBCE-4B93-AC56-03697F375A04@gmail.com>

Dear all

I?m working on a manuscript and would like to know what should be the proper referencing of the MINC toolkit itself? (besides of course, specific papers on post-processing techniques)

Thanks
Pedro


From louis.collins at mcgill.ca  Thu Jul 27 17:21:59 2017
From: louis.collins at mcgill.ca (Louis Collins, Dr.)
Date: Thu, 27 Jul 2017 21:21:59 +0000
Subject: [MINC-users] Proper citation
In-Reply-To: <C2554A26-BBCE-4B93-AC56-03697F375A04@gmail.com>
References: <C2554A26-BBCE-4B93-AC56-03697F375A04@gmail.com>
Message-ID: <A8A4ACA5-BD95-4F7A-95E5-58C8517BF9AE@mcgill.ca>

Pedro,

I don?t know of a single reference that does justice to all the minc software.  

I think it is best to reference the individual pieces of software to give credit to the authors of each tool used.

-Louis


> On Jul 27, 2017, at 3:24 PM, Pedro <ptcougopinto at gmail.com> wrote:
> 
> Dear all
> 
> I?m working on a manuscript and would like to know what should be the proper referencing of the MINC toolkit itself? (besides of course, specific papers on post-processing techniques)
> 
> Thanks
> Pedro
> 
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


From bert at phalarope.com  Thu Jul 27 17:34:41 2017
From: bert at phalarope.com (Robert D. Vincent)
Date: Thu, 27 Jul 2017 17:34:41 -0400
Subject: [MINC-users] Proper citation
In-Reply-To: <C2554A26-BBCE-4B93-AC56-03697F375A04@gmail.com>
References: <C2554A26-BBCE-4B93-AC56-03697F375A04@gmail.com>
Message-ID: <CAAd5DeTTNyeAq1pu-R3Au5L3L9yQp=EwqdUyzxotq_xhMQx7YQ@mail.gmail.com>

Hi Pedro,

You might want to cite:

http://journal.frontiersin.org/article/10.3389/fninf.2016.00035/

    -bert

On Jul 27, 2017 3:26 PM, "Pedro" <ptcougopinto at gmail.com> wrote:

> Dear all
>
> I?m working on a manuscript and would like to know what should be the
> proper referencing of the MINC toolkit itself? (besides of course, specific
> papers on post-processing techniques)
>
> Thanks
> Pedro
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>