From andrew at biospective.com  Wed Aug  5 09:41:15 2015
From: andrew at biospective.com (Andrew Wood)
Date: Wed, 5 Aug 2015 09:41:15 -0400
Subject: [MINC-users] Visualizing data with high dynamic range
Message-ID: <CABApf9EHgXNTbPi5qqxHJq4GNrH+1jff-YHNf0K53SabCnFTnQ@mail.gmail.com>

Hi all,

I'm having trouble visualizing a volume containing float data with a high
dynamic range. Both register and Display discretize the signal (down to
byte precision?), which is not workable for these volumes.

The only solution I have right now is to explode the data into new volumes
by sliding a reduced range over the signal, clamping away data that
register and Display can't handle.

Does anyone have experience visualizing high dynamic range data? Is there a
tool that can do this, or just a better workaround?

Thanks,
Andrew

From robert.d.vincent at mcgill.ca  Wed Aug  5 10:45:04 2015
From: robert.d.vincent at mcgill.ca (Robert D. Vincent)
Date: Wed, 5 Aug 2015 10:45:04 -0400
Subject: [MINC-users] Visualizing data with high dynamic range
In-Reply-To: <CABApf9EHgXNTbPi5qqxHJq4GNrH+1jff-YHNf0K53SabCnFTnQ@mail.gmail.com>
References: <CABApf9EHgXNTbPi5qqxHJq4GNrH+1jff-YHNf0K53SabCnFTnQ@mail.gmail.com>
Message-ID: <CAAd5DeRo2B_jy7dCHmWPEoxi93mg7d0ot_gfcJ5+vHVTjXCNyA@mail.gmail.com>

Hi Andrew,

Display should be able to handle high dynamic range data. There is a global
variable "Convert_volumes_to_byte" which is true by default, but which can
be overridden either on the command line or the Display.globals
initialization file. You can set it either by specifying:

Display -global Convert_volumes_to_byte false <input.mnc>

or by adding the line:

Convert_volumes_to_byte=False;

to a file named Display.globals in your home directory.

Register has similar functionality, but it was added fairly recently, so I
don't believe it is widely available. The code checked into Github supports
two globals, Volume_voxel_type and Volume_voxel_signed, that control the
conversion of loaded volumes.

Hope this helps. I intend to change the default behavior in future versions
of Display, but I haven't made the change yet.

    -bert

On Wed, Aug 5, 2015 at 9:41 AM, Andrew Wood <andrew at biospective.com> wrote:

> Hi all,
>
> I'm having trouble visualizing a volume containing float data with a high
> dynamic range. Both register and Display discretize the signal (down to
> byte precision?), which is not workable for these volumes.
>
> The only solution I have right now is to explode the data into new volumes
> by sliding a reduced range over the signal, clamping away data that
> register and Display can't handle.
>
> Does anyone have experience visualizing high dynamic range data? Is there a
> tool that can do this, or just a better workaround?
>
> Thanks,
> Andrew
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From claude at bic.mni.mcgill.ca  Wed Aug  5 11:07:26 2015
From: claude at bic.mni.mcgill.ca (Claude LEPAGE)
Date: Wed, 5 Aug 2015 11:07:26 -0400
Subject: [MINC-users] Visualizing data with high dynamic range
In-Reply-To: <CABApf9EHgXNTbPi5qqxHJq4GNrH+1jff-YHNf0K53SabCnFTnQ@mail.gmail.com>
Message-ID: <201508051507.t75F7QDc029273@login2.bic.mni.mcgill.ca>

Andrew,

For viewing purposes, I would suggest to take the log of your image.

minccalc -expression 'log(1.0+abs(A[0]))' in.mnc out.mnc

Beware of A[0]==0 to avoid the singularity.

Claude


>
> Hi all,
>
> I'm having trouble visualizing a volume containing float data with a high
> dynamic range. Both register and Display discretize the signal (down to
> byte precision?), which is not workable for these volumes.
>
> The only solution I have right now is to explode the data into new volumes
> by sliding a reduced range over the signal, clamping away data that
> register and Display can't handle.
>
> Does anyone have experience visualizing high dynamic range data? Is there a
> tool that can do this, or just a better workaround?
>
> Thanks,
> Andrew
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From gdevenyi at gmail.com  Wed Aug  5 11:37:22 2015
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Wed, 5 Aug 2015 11:37:22 -0400
Subject: [MINC-users] Determining DICOM Series File Members?
Message-ID: <CAFQOoOoZgf8SVOd2L5FR_YVVD+j8WHrXz-MKNuibZk1OWiyr5Q@mail.gmail.com>

Hi all,

If I have a large collection of DICOM files from a single scanning session
(~1000 files), does anyone know of a way to pick out the files of a
specific series? i.e. I have a bunch of scan types and I want to know which
files are the DICOMs for T1s?

Thanks.

-- 
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
McGill University
t: 514.761.6131x4781
e: gdevenyi at gmail.com

From jon at pipitone.ca  Wed Aug  5 11:49:35 2015
From: jon at pipitone.ca (Jon Pipitone)
Date: Wed, 5 Aug 2015 11:49:35 -0400
Subject: [MINC-users] Determining DICOM Series File Members?
In-Reply-To: <CAFQOoOoZgf8SVOd2L5FR_YVVD+j8WHrXz-MKNuibZk1OWiyr5Q@mail.gmail.com>
References: <CAFQOoOoZgf8SVOd2L5FR_YVVD+j8WHrXz-MKNuibZk1OWiyr5Q@mail.gmail.com>
Message-ID: <20150805154927.GB46536@kandel.kimel.ric>

We've been dealing with this in a pretty stupid but functional way:
regexs on the StudyDescription field. The descriptions varies from
scanner to scanner, and tech to tech, of course, so you have to tweak
your library of regexs as you encounter new data but, you know, it
works. :-)

pydicom is your friend for this. 

Jon.

On 08/05, Gabriel A. Devenyi wrote:
> Hi all,
> 
> If I have a large collection of DICOM files from a single scanning session
> (~1000 files), does anyone know of a way to pick out the files of a
> specific series? i.e. I have a bunch of scan types and I want to know which
> files are the DICOMs for T1s?
> 
> Thanks.
> 
> -- 
> Gabriel A. Devenyi B.Eng. Ph.D.
> Research Computing Associate
> Computational Brain Anatomy Laboratory
> Cerebral Imaging Center
> Douglas Mental Health University Institute
> McGill University
> t: 514.761.6131x4781
> e: gdevenyi at gmail.com
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From andrew at biospective.com  Wed Aug  5 11:51:42 2015
From: andrew at biospective.com (Andrew Wood)
Date: Wed, 5 Aug 2015 11:51:42 -0400
Subject: [MINC-users] Determining DICOM Series File Members?
In-Reply-To: <20150805154927.GB46536@kandel.kimel.ric>
References: <CAFQOoOoZgf8SVOd2L5FR_YVVD+j8WHrXz-MKNuibZk1OWiyr5Q@mail.gmail.com>
	<20150805154927.GB46536@kandel.kimel.ric>
Message-ID: <CABApf9GhZPRt5d-ZmKSknAxrkjx_Yyip1fwzkHRqd2s9WOzkCw@mail.gmail.com>

Hi Gabriel,

This is a pretty dumb way to do it, but here's what I run:

$ dcmdump +P 0008,103e +F * | grep MySequenceName -B 1 | grep dcmdump | awk
'{print $NF}'

- Andrew

On Wed, Aug 5, 2015 at 11:49 AM, Jon Pipitone <jon at pipitone.ca> wrote:

> We've been dealing with this in a pretty stupid but functional way:
> regexs on the StudyDescription field. The descriptions varies from
> scanner to scanner, and tech to tech, of course, so you have to tweak
> your library of regexs as you encounter new data but, you know, it
> works. :-)
>
> pydicom is your friend for this.
>
> Jon.
>
> On 08/05, Gabriel A. Devenyi wrote:
> > Hi all,
> >
> > If I have a large collection of DICOM files from a single scanning
> session
> > (~1000 files), does anyone know of a way to pick out the files of a
> > specific series? i.e. I have a bunch of scan types and I want to know
> which
> > files are the DICOMs for T1s?
> >
> > Thanks.
> >
> > --
> > Gabriel A. Devenyi B.Eng. Ph.D.
> > Research Computing Associate
> > Computational Brain Anatomy Laboratory
> > Cerebral Imaging Center
> > Douglas Mental Health University Institute
> > McGill University
> > t: 514.761.6131x4781
> > e: gdevenyi at gmail.com
> > _______________________________________________
> > 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 gdevenyi at gmail.com  Wed Aug  5 11:54:17 2015
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Wed, 5 Aug 2015 11:54:17 -0400
Subject: [MINC-users] Determining DICOM Series File Members?
In-Reply-To: <CABApf9GhZPRt5d-ZmKSknAxrkjx_Yyip1fwzkHRqd2s9WOzkCw@mail.gmail.com>
References: <CAFQOoOoZgf8SVOd2L5FR_YVVD+j8WHrXz-MKNuibZk1OWiyr5Q@mail.gmail.com>
	<20150805154927.GB46536@kandel.kimel.ric>
	<CABApf9GhZPRt5d-ZmKSknAxrkjx_Yyip1fwzkHRqd2s9WOzkCw@mail.gmail.com>
Message-ID: <CAFQOoOqjuUwTMRYUsOGoVBochVeFHe9t11TB4VkwnBTSUviA2A@mail.gmail.com>

Thanks for the quick replies!

As is usually the case, I can across another Andrew Janke tool
https://github.com/andrewjanke/mnc2dcm

dcmsort does exactly what i'm looking for

-- 
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
McGill University
t: 514.761.6131x4781
e: gdevenyi at gmail.com

On Wed, Aug 5, 2015 at 11:51 AM, Andrew Wood <andrew at biospective.com> wrote:

> Hi Gabriel,
>
> This is a pretty dumb way to do it, but here's what I run:
>
> $ dcmdump +P 0008,103e +F * | grep MySequenceName -B 1 | grep dcmdump | awk
> '{print $NF}'
>
> - Andrew
>
> On Wed, Aug 5, 2015 at 11:49 AM, Jon Pipitone <jon at pipitone.ca> wrote:
>
> > We've been dealing with this in a pretty stupid but functional way:
> > regexs on the StudyDescription field. The descriptions varies from
> > scanner to scanner, and tech to tech, of course, so you have to tweak
> > your library of regexs as you encounter new data but, you know, it
> > works. :-)
> >
> > pydicom is your friend for this.
> >
> > Jon.
> >
> > On 08/05, Gabriel A. Devenyi wrote:
> > > Hi all,
> > >
> > > If I have a large collection of DICOM files from a single scanning
> > session
> > > (~1000 files), does anyone know of a way to pick out the files of a
> > > specific series? i.e. I have a bunch of scan types and I want to know
> > which
> > > files are the DICOMs for T1s?
> > >
> > > Thanks.
> > >
> > > --
> > > Gabriel A. Devenyi B.Eng. Ph.D.
> > > Research Computing Associate
> > > Computational Brain Anatomy Laboratory
> > > Cerebral Imaging Center
> > > Douglas Mental Health University Institute
> > > McGill University
> > > t: 514.761.6131x4781
> > > e: gdevenyi at gmail.com
> > > _______________________________________________
> > > 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 jon at pipitone.ca  Wed Aug  5 12:11:10 2015
From: jon at pipitone.ca (Jon Pipitone)
Date: Wed, 5 Aug 2015 12:11:10 -0400
Subject: [MINC-users] Determining DICOM Series File Members?
In-Reply-To: <CAFQOoOqjuUwTMRYUsOGoVBochVeFHe9t11TB4VkwnBTSUviA2A@mail.gmail.com>
References: <CAFQOoOoZgf8SVOd2L5FR_YVVD+j8WHrXz-MKNuibZk1OWiyr5Q@mail.gmail.com>
	<20150805154927.GB46536@kandel.kimel.ric>
	<CABApf9GhZPRt5d-ZmKSknAxrkjx_Yyip1fwzkHRqd2s9WOzkCw@mail.gmail.com>
	<CAFQOoOqjuUwTMRYUsOGoVBochVeFHe9t11TB4VkwnBTSUviA2A@mail.gmail.com>
Message-ID: <20150805161109.GA17454@kandel.kimel.ric>

Ah, I think I misunderstood. You don't want to determine whether a dicom
is from a T1 or T2 or etc... just group together all of the dicoms from
each series (or a specific series) by number? 

Jon. 

On 08/05, Gabriel A. Devenyi wrote:
> Thanks for the quick replies!
> 
> As is usually the case, I can across another Andrew Janke tool
> https://github.com/andrewjanke/mnc2dcm
> 
> dcmsort does exactly what i'm looking for
> 
> -- 
> Gabriel A. Devenyi B.Eng. Ph.D.
> Research Computing Associate
> Computational Brain Anatomy Laboratory
> Cerebral Imaging Center
> Douglas Mental Health University Institute
> McGill University
> t: 514.761.6131x4781
> e: gdevenyi at gmail.com
> 
> On Wed, Aug 5, 2015 at 11:51 AM, Andrew Wood <andrew at biospective.com> wrote:
> 
> > Hi Gabriel,
> >
> > This is a pretty dumb way to do it, but here's what I run:
> >
> > $ dcmdump +P 0008,103e +F * | grep MySequenceName -B 1 | grep dcmdump | awk
> > '{print $NF}'
> >
> > - Andrew
> >
> > On Wed, Aug 5, 2015 at 11:49 AM, Jon Pipitone <jon at pipitone.ca> wrote:
> >
> > > We've been dealing with this in a pretty stupid but functional way:
> > > regexs on the StudyDescription field. The descriptions varies from
> > > scanner to scanner, and tech to tech, of course, so you have to tweak
> > > your library of regexs as you encounter new data but, you know, it
> > > works. :-)
> > >
> > > pydicom is your friend for this.
> > >
> > > Jon.
> > >
> > > On 08/05, Gabriel A. Devenyi wrote:
> > > > Hi all,
> > > >
> > > > If I have a large collection of DICOM files from a single scanning
> > > session
> > > > (~1000 files), does anyone know of a way to pick out the files of a
> > > > specific series? i.e. I have a bunch of scan types and I want to know
> > > which
> > > > files are the DICOMs for T1s?
> > > >
> > > > Thanks.
> > > >
> > > > --
> > > > Gabriel A. Devenyi B.Eng. Ph.D.
> > > > Research Computing Associate
> > > > Computational Brain Anatomy Laboratory
> > > > Cerebral Imaging Center
> > > > Douglas Mental Health University Institute
> > > > McGill University
> > > > t: 514.761.6131x4781
> > > > e: gdevenyi at gmail.com
> > > > _______________________________________________
> > > > 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 gdevenyi at gmail.com  Wed Aug  5 12:19:19 2015
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Wed, 5 Aug 2015 12:19:19 -0400
Subject: [MINC-users] Determining DICOM Series File Members?
In-Reply-To: <20150805161109.GA17454@kandel.kimel.ric>
References: <CAFQOoOoZgf8SVOd2L5FR_YVVD+j8WHrXz-MKNuibZk1OWiyr5Q@mail.gmail.com>
	<20150805154927.GB46536@kandel.kimel.ric>
	<CABApf9GhZPRt5d-ZmKSknAxrkjx_Yyip1fwzkHRqd2s9WOzkCw@mail.gmail.com>
	<CAFQOoOqjuUwTMRYUsOGoVBochVeFHe9t11TB4VkwnBTSUviA2A@mail.gmail.com>
	<20150805161109.GA17454@kandel.kimel.ric>
Message-ID: <CAFQOoOpBy4LZS=7LaqZRb2O-b7p2GZBXnvvqhXaV7ZxWA90EwA@mail.gmail.com>

I did want to know which series corresponds to T1 etc, turns out dicomsort
does that *and* sorts it into nice directories for me, which is very
convenient. The directories it creates are named the series name as well.

-- 
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
McGill University
t: 514.761.6131x4781
e: gdevenyi at gmail.com

On Wed, Aug 5, 2015 at 12:11 PM, Jon Pipitone <jon at pipitone.ca> wrote:

> Ah, I think I misunderstood. You don't want to determine whether a dicom
> is from a T1 or T2 or etc... just group together all of the dicoms from
> each series (or a specific series) by number?
>
> Jon.
>
> On 08/05, Gabriel A. Devenyi wrote:
> > Thanks for the quick replies!
> >
> > As is usually the case, I can across another Andrew Janke tool
> > https://github.com/andrewjanke/mnc2dcm
> >
> > dcmsort does exactly what i'm looking for
> >
> > --
> > Gabriel A. Devenyi B.Eng. Ph.D.
> > Research Computing Associate
> > Computational Brain Anatomy Laboratory
> > Cerebral Imaging Center
> > Douglas Mental Health University Institute
> > McGill University
> > t: 514.761.6131x4781
> > e: gdevenyi at gmail.com
> >
> > On Wed, Aug 5, 2015 at 11:51 AM, Andrew Wood <andrew at biospective.com>
> wrote:
> >
> > > Hi Gabriel,
> > >
> > > This is a pretty dumb way to do it, but here's what I run:
> > >
> > > $ dcmdump +P 0008,103e +F * | grep MySequenceName -B 1 | grep dcmdump
> | awk
> > > '{print $NF}'
> > >
> > > - Andrew
> > >
> > > On Wed, Aug 5, 2015 at 11:49 AM, Jon Pipitone <jon at pipitone.ca> wrote:
> > >
> > > > We've been dealing with this in a pretty stupid but functional way:
> > > > regexs on the StudyDescription field. The descriptions varies from
> > > > scanner to scanner, and tech to tech, of course, so you have to tweak
> > > > your library of regexs as you encounter new data but, you know, it
> > > > works. :-)
> > > >
> > > > pydicom is your friend for this.
> > > >
> > > > Jon.
> > > >
> > > > On 08/05, Gabriel A. Devenyi wrote:
> > > > > Hi all,
> > > > >
> > > > > If I have a large collection of DICOM files from a single scanning
> > > > session
> > > > > (~1000 files), does anyone know of a way to pick out the files of a
> > > > > specific series? i.e. I have a bunch of scan types and I want to
> know
> > > > which
> > > > > files are the DICOMs for T1s?
> > > > >
> > > > > Thanks.
> > > > >
> > > > > --
> > > > > Gabriel A. Devenyi B.Eng. Ph.D.
> > > > > Research Computing Associate
> > > > > Computational Brain Anatomy Laboratory
> > > > > Cerebral Imaging Center
> > > > > Douglas Mental Health University Institute
> > > > > McGill University
> > > > > t: 514.761.6131x4781
> > > > > e: gdevenyi at gmail.com
> > > > > _______________________________________________
> > > > > 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 robert.d.vincent at mcgill.ca  Wed Aug  5 16:00:22 2015
From: robert.d.vincent at mcgill.ca (Robert D. Vincent)
Date: Wed, 5 Aug 2015 16:00:22 -0400
Subject: [MINC-users] Histogram stats
In-Reply-To: <A7E92A11-566A-4079-8FD4-54C2512DAA53@gmail.com>
References: <CAACqNXu5KBVAEjZKbBh8Um_02KjV=zichowkv5d+ScxRQOQXQw@mail.gmail.com>
	<CAG0CB20bn1ZR-SMGeben+Nr7hP3XqHsXUWEg_cG-VzcHpZDETw@mail.gmail.com>
	<A7E92A11-566A-4079-8FD4-54C2512DAA53@gmail.com>
Message-ID: <CAAd5DeT0-=1XJCxPgUa19Dkevb+XQFdr_8FhkOxxVsW7RpDnrA@mail.gmail.com>

Hi Pedro,

In response to this, I just added skewness and kurtosis options to
mincstats.c on the "develop" branch:

https://github.com/BIC-MNI/minc-tools/blob/develop/progs/mincstats/mincstats.c

Hope this is useful,

    -bert


On Sun, Jul 26, 2015 at 2:13 PM, Pedro Pinto <ptcougopinto at gmail.com> wrote:

> Thanks, I?ll look into both options. Thanks for pointing the code
> location, Andrew.
> Pedro
>
>
> On 25, Jul2015, at 11:34, Andrew Janke <a.janke at gmail.com> wrote:
>
> > Hi Pedro,
> >
> > You are correct, there is no calculation of kurtosis or skewness in
> > mincstats. That said if you are after simple sample kurtosis it would
> > be easy to add the calculation of the 3rd moment in mincstats here:
> >
> >
> https://github.com/BIC-MNI/minc-tools/blob/master/progs/mincstats/mincstats.c#L1360
> >
> >
> > a
> >
> >
> > On 25 July 2015 at 07:18, Pedro Telles Cougo-Pinto
> > <ptcougopinto at gmail.com> wrote:
> >> Dear all,
> >>
> >> Is it possible to obtain skewness and kurtosis summary measures from
> MINC
> >> volumes? As far as I could see, mincstats does not offer this option.
> >>
> >> Thanks,
> >> Pedro
> >> _______________________________________________
> >> 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 gdevenyi at gmail.com  Wed Aug  5 16:42:04 2015
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Wed, 5 Aug 2015 16:42:04 -0400
Subject: [MINC-users] Display.globals options was: Re: Visualizing data with
 high dynamic range
Message-ID: <CAFQOoOpZAqRu+NShxjTnNMK+wj3q9+r=r51hcqqbhqy0sJ5njA@mail.gmail.com>

Bert,

Are there docs somewhere on what we can specify for Display.globals?

-- 
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
McGill University
t: 514.761.6131x4781
e: gdevenyi at gmail.com

On Wed, Aug 5, 2015 at 10:45 AM, Robert D. Vincent <
robert.d.vincent at mcgill.ca> wrote:

> Hi Andrew,
>
> Display should be able to handle high dynamic range data. There is a global
> variable "Convert_volumes_to_byte" which is true by default, but which can
> be overridden either on the command line or the Display.globals
> initialization file. You can set it either by specifying:
>
> Display -global Convert_volumes_to_byte false <input.mnc>
>
> or by adding the line:
>
> Convert_volumes_to_byte=False;
>
> to a file named Display.globals in your home directory.
>
> Register has similar functionality, but it was added fairly recently, so I
> don't believe it is widely available. The code checked into Github supports
> two globals, Volume_voxel_type and Volume_voxel_signed, that control the
> conversion of loaded volumes.
>
> Hope this helps. I intend to change the default behavior in future versions
> of Display, but I haven't made the change yet.
>
>     -bert
>
> On Wed, Aug 5, 2015 at 9:41 AM, Andrew Wood <andrew at biospective.com>
> wrote:
>
> > Hi all,
> >
> > I'm having trouble visualizing a volume containing float data with a high
> > dynamic range. Both register and Display discretize the signal (down to
> > byte precision?), which is not workable for these volumes.
> >
> > The only solution I have right now is to explode the data into new
> volumes
> > by sliding a reduced range over the signal, clamping away data that
> > register and Display can't handle.
> >
> > Does anyone have experience visualizing high dynamic range data? Is
> there a
> > tool that can do this, or just a better workaround?
> >
> > 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 vladimir.fonov at gmail.com  Wed Aug  5 17:01:56 2015
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Wed, 05 Aug 2015 17:01:56 -0400
Subject: [MINC-users] Display.globals options was: Re: Visualizing data
 with high dynamic range
In-Reply-To: <CAFQOoOpZAqRu+NShxjTnNMK+wj3q9+r=r51hcqqbhqy0sJ5njA@mail.gmail.com>
References: <CAFQOoOpZAqRu+NShxjTnNMK+wj3q9+r=r51hcqqbhqy0sJ5njA@mail.gmail.com>
Message-ID: <55C279C4.1070700@gmail.com>

Hello,


https://github.com/BIC-MNI/Display/blob/master/Display.globals - not 
much documentation though.


On 15-08-05 04:42 PM, Gabriel A. Devenyi wrote:
> Bert,
>
> Are there docs somewhere on what we can specify for Display.globals?
>


-- 
Best regards,

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

From a.janke at gmail.com  Wed Aug  5 21:25:38 2015
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 6 Aug 2015 11:25:38 +1000
Subject: [MINC-users] Histogram stats
In-Reply-To: <CAAd5DeT0-=1XJCxPgUa19Dkevb+XQFdr_8FhkOxxVsW7RpDnrA@mail.gmail.com>
References: <CAACqNXu5KBVAEjZKbBh8Um_02KjV=zichowkv5d+ScxRQOQXQw@mail.gmail.com>
	<CAG0CB20bn1ZR-SMGeben+Nr7hP3XqHsXUWEg_cG-VzcHpZDETw@mail.gmail.com>
	<A7E92A11-566A-4079-8FD4-54C2512DAA53@gmail.com>
	<CAAd5DeT0-=1XJCxPgUa19Dkevb+XQFdr_8FhkOxxVsW7RpDnrA@mail.gmail.com>
Message-ID: <CAG0CB22tOo0JBVFXiHKYwHaG3vJMcujd+iVoRGY9EJRthBJQoA@mail.gmail.com>

Thanks Bert,

I have updated the manual page to suit (but not tested it yet as I did
it in the online github editor thing).

   https://github.com/BIC-MNI/minc-tools/commit/ff793f4f61c37aed2ed7c265e9e515bda5e9a213

I also added the extra thresholding arguments you put in a while back!
 (otsu/kaput/kittle/simple).

ta


a


On 6 August 2015 at 06:00, Robert D. Vincent <robert.d.vincent at mcgill.ca> wrote:
> Hi Pedro,
>
> In response to this, I just added skewness and kurtosis options to
> mincstats.c on the "develop" branch:
>
> https://github.com/BIC-MNI/minc-tools/blob/develop/progs/mincstats/mincstats.c
>
> Hope this is useful,
>
>     -bert
>
>
> On Sun, Jul 26, 2015 at 2:13 PM, Pedro Pinto <ptcougopinto at gmail.com> wrote:
>
>> Thanks, I?ll look into both options. Thanks for pointing the code
>> location, Andrew.
>> Pedro
>>
>>
>> On 25, Jul2015, at 11:34, Andrew Janke <a.janke at gmail.com> wrote:
>>
>> > Hi Pedro,
>> >
>> > You are correct, there is no calculation of kurtosis or skewness in
>> > mincstats. That said if you are after simple sample kurtosis it would
>> > be easy to add the calculation of the 3rd moment in mincstats here:
>> >
>> >
>> https://github.com/BIC-MNI/minc-tools/blob/master/progs/mincstats/mincstats.c#L1360
>> >
>> >
>> > a
>> >
>> >
>> > On 25 July 2015 at 07:18, Pedro Telles Cougo-Pinto
>> > <ptcougopinto at gmail.com> wrote:
>> >> Dear all,
>> >>
>> >> Is it possible to obtain skewness and kurtosis summary measures from
>> MINC
>> >> volumes? As far as I could see, mincstats does not offer this option.
>> >>
>> >> Thanks,
>> >> Pedro
>> >> _______________________________________________
>> >> 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 a.janke at gmail.com  Wed Aug  5 21:51:19 2015
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 6 Aug 2015 11:51:19 +1000
Subject: [MINC-users] Determining DICOM Series File Members?
In-Reply-To: <CAFQOoOpBy4LZS=7LaqZRb2O-b7p2GZBXnvvqhXaV7ZxWA90EwA@mail.gmail.com>
References: <CAFQOoOoZgf8SVOd2L5FR_YVVD+j8WHrXz-MKNuibZk1OWiyr5Q@mail.gmail.com>
	<20150805154927.GB46536@kandel.kimel.ric>
	<CABApf9GhZPRt5d-ZmKSknAxrkjx_Yyip1fwzkHRqd2s9WOzkCw@mail.gmail.com>
	<CAFQOoOqjuUwTMRYUsOGoVBochVeFHe9t11TB4VkwnBTSUviA2A@mail.gmail.com>
	<20150805161109.GA17454@kandel.kimel.ric>
	<CAFQOoOpBy4LZS=7LaqZRb2O-b7p2GZBXnvvqhXaV7ZxWA90EwA@mail.gmail.com>
Message-ID: <CAG0CB22Gs4m66qaoNETWX5Pty33rSZ3nft=eAwfh1v6beWcBGQ@mail.gmail.com>

Beat me to it...

The only wrinkle is that it uses DICOM.pm (and my mods of it), I had
always planned to port it to use dcmdump from dcmtk but never got to
it. Be sure to use the --rename_log option, it makes life easier if
things go awry!


a


On 6 August 2015 at 02:19, Gabriel A. Devenyi <gdevenyi at gmail.com> wrote:
> I did want to know which series corresponds to T1 etc, turns out dicomsort
> does that *and* sorts it into nice directories for me, which is very
> convenient. The directories it creates are named the series name as well.
>
> --
> Gabriel A. Devenyi B.Eng. Ph.D.
> Research Computing Associate
> Computational Brain Anatomy Laboratory
> Cerebral Imaging Center
> Douglas Mental Health University Institute
> McGill University
> t: 514.761.6131x4781
> e: gdevenyi at gmail.com
>
> On Wed, Aug 5, 2015 at 12:11 PM, Jon Pipitone <jon at pipitone.ca> wrote:
>
>> Ah, I think I misunderstood. You don't want to determine whether a dicom
>> is from a T1 or T2 or etc... just group together all of the dicoms from
>> each series (or a specific series) by number?
>>
>> Jon.
>>
>> On 08/05, Gabriel A. Devenyi wrote:
>> > Thanks for the quick replies!
>> >
>> > As is usually the case, I can across another Andrew Janke tool
>> > https://github.com/andrewjanke/mnc2dcm
>> >
>> > dcmsort does exactly what i'm looking for
>> >
>> > --
>> > Gabriel A. Devenyi B.Eng. Ph.D.
>> > Research Computing Associate
>> > Computational Brain Anatomy Laboratory
>> > Cerebral Imaging Center
>> > Douglas Mental Health University Institute
>> > McGill University
>> > t: 514.761.6131x4781
>> > e: gdevenyi at gmail.com
>> >
>> > On Wed, Aug 5, 2015 at 11:51 AM, Andrew Wood <andrew at biospective.com>
>> wrote:
>> >
>> > > Hi Gabriel,
>> > >
>> > > This is a pretty dumb way to do it, but here's what I run:
>> > >
>> > > $ dcmdump +P 0008,103e +F * | grep MySequenceName -B 1 | grep dcmdump
>> | awk
>> > > '{print $NF}'
>> > >
>> > > - Andrew
>> > >
>> > > On Wed, Aug 5, 2015 at 11:49 AM, Jon Pipitone <jon at pipitone.ca> wrote:
>> > >
>> > > > We've been dealing with this in a pretty stupid but functional way:
>> > > > regexs on the StudyDescription field. The descriptions varies from
>> > > > scanner to scanner, and tech to tech, of course, so you have to tweak
>> > > > your library of regexs as you encounter new data but, you know, it
>> > > > works. :-)
>> > > >
>> > > > pydicom is your friend for this.
>> > > >
>> > > > Jon.
>> > > >
>> > > > On 08/05, Gabriel A. Devenyi wrote:
>> > > > > Hi all,
>> > > > >
>> > > > > If I have a large collection of DICOM files from a single scanning
>> > > > session
>> > > > > (~1000 files), does anyone know of a way to pick out the files of a
>> > > > > specific series? i.e. I have a bunch of scan types and I want to
>> know
>> > > > which
>> > > > > files are the DICOMs for T1s?
>> > > > >
>> > > > > Thanks.
>> > > > >
>> > > > > --
>> > > > > Gabriel A. Devenyi B.Eng. Ph.D.
>> > > > > Research Computing Associate
>> > > > > Computational Brain Anatomy Laboratory
>> > > > > Cerebral Imaging Center
>> > > > > Douglas Mental Health University Institute
>> > > > > McGill University
>> > > > > t: 514.761.6131x4781
>> > > > > e: gdevenyi at gmail.com
>> > > > > _______________________________________________
>> > > > > 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

From robert.d.vincent at mcgill.ca  Thu Aug  6 12:53:39 2015
From: robert.d.vincent at mcgill.ca (Robert D. Vincent)
Date: Thu, 6 Aug 2015 12:53:39 -0400
Subject: [MINC-users] Display.globals options was: Re: Visualizing data
 with high dynamic range
In-Reply-To: <CAFQOoOpZAqRu+NShxjTnNMK+wj3q9+r=r51hcqqbhqy0sJ5njA@mail.gmail.com>
References: <CAFQOoOpZAqRu+NShxjTnNMK+wj3q9+r=r51hcqqbhqy0sJ5njA@mail.gmail.com>
Message-ID: <CAAd5DeTMVh3nHO+L-WFGR0pkQKPbbwYDWpVy=qUS3-Z5fQvAjg@mail.gmail.com>

Hi Gabriel,

There's no real documentation on this. There has been some recent work on
improving the Display manual, which I hope to release sometime in the next
few months. I'll make it a point to add documentation of some of the more
"interesting" globals.

    -bert

On Wed, Aug 5, 2015 at 4:42 PM, Gabriel A. Devenyi <gdevenyi at gmail.com>
wrote:

> Bert,
>
> Are there docs somewhere on what we can specify for Display.globals?
>
> --
> Gabriel A. Devenyi B.Eng. Ph.D.
> Research Computing Associate
> Computational Brain Anatomy Laboratory
> Cerebral Imaging Center
> Douglas Mental Health University Institute
> McGill University
> t: 514.761.6131x4781
> e: gdevenyi at gmail.com
>
> On Wed, Aug 5, 2015 at 10:45 AM, Robert D. Vincent <
> robert.d.vincent at mcgill.ca> wrote:
>
> > Hi Andrew,
> >
> > Display should be able to handle high dynamic range data. There is a
> global
> > variable "Convert_volumes_to_byte" which is true by default, but which
> can
> > be overridden either on the command line or the Display.globals
> > initialization file. You can set it either by specifying:
> >
> > Display -global Convert_volumes_to_byte false <input.mnc>
> >
> > or by adding the line:
> >
> > Convert_volumes_to_byte=False;
> >
> > to a file named Display.globals in your home directory.
> >
> > Register has similar functionality, but it was added fairly recently, so
> I
> > don't believe it is widely available. The code checked into Github
> supports
> > two globals, Volume_voxel_type and Volume_voxel_signed, that control the
> > conversion of loaded volumes.
> >
> > Hope this helps. I intend to change the default behavior in future
> versions
> > of Display, but I haven't made the change yet.
> >
> >     -bert
> >
> > On Wed, Aug 5, 2015 at 9:41 AM, Andrew Wood <andrew at biospective.com>
> > wrote:
> >
> > > Hi all,
> > >
> > > I'm having trouble visualizing a volume containing float data with a
> high
> > > dynamic range. Both register and Display discretize the signal (down to
> > > byte precision?), which is not workable for these volumes.
> > >
> > > The only solution I have right now is to explode the data into new
> > volumes
> > > by sliding a reduced range over the signal, clamping away data that
> > > register and Display can't handle.
> > >
> > > Does anyone have experience visualizing high dynamic range data? Is
> > there a
> > > tool that can do this, or just a better workaround?
> > >
> > > 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 ptcougopinto at gmail.com  Thu Aug  6 13:00:58 2015
From: ptcougopinto at gmail.com (Pedro Telles Cougo-Pinto)
Date: Thu, 6 Aug 2015 14:00:58 -0300
Subject: [MINC-users] Histogram stats
In-Reply-To: <CAAd5DeT0-=1XJCxPgUa19Dkevb+XQFdr_8FhkOxxVsW7RpDnrA@mail.gmail.com>
References: <CAACqNXu5KBVAEjZKbBh8Um_02KjV=zichowkv5d+ScxRQOQXQw@mail.gmail.com>
	<CAG0CB20bn1ZR-SMGeben+Nr7hP3XqHsXUWEg_cG-VzcHpZDETw@mail.gmail.com>
	<A7E92A11-566A-4079-8FD4-54C2512DAA53@gmail.com>
	<CAAd5DeT0-=1XJCxPgUa19Dkevb+XQFdr_8FhkOxxVsW7RpDnrA@mail.gmail.com>
Message-ID: <CAACqNXvBDvF0==wfBF3G844PKBqvJfBT3oCN+-NDBr+9xK_=0w@mail.gmail.com>

Fantastic. Thanks!
Pedro

2015-08-05 17:00 GMT-03:00 Robert D. Vincent <robert.d.vincent at mcgill.ca>:

> Hi Pedro,
>
> In response to this, I just added skewness and kurtosis options to
> mincstats.c on the "develop" branch:
>
>
> https://github.com/BIC-MNI/minc-tools/blob/develop/progs/mincstats/mincstats.c
>
> Hope this is useful,
>
>     -bert
>
>
> On Sun, Jul 26, 2015 at 2:13 PM, Pedro Pinto <ptcougopinto at gmail.com>
> wrote:
>
> > Thanks, I?ll look into both options. Thanks for pointing the code
> > location, Andrew.
> > Pedro
> >
> >
> > On 25, Jul2015, at 11:34, Andrew Janke <a.janke at gmail.com> wrote:
> >
> > > Hi Pedro,
> > >
> > > You are correct, there is no calculation of kurtosis or skewness in
> > > mincstats. That said if you are after simple sample kurtosis it would
> > > be easy to add the calculation of the 3rd moment in mincstats here:
> > >
> > >
> >
> https://github.com/BIC-MNI/minc-tools/blob/master/progs/mincstats/mincstats.c#L1360
> > >
> > >
> > > a
> > >
> > >
> > > On 25 July 2015 at 07:18, Pedro Telles Cougo-Pinto
> > > <ptcougopinto at gmail.com> wrote:
> > >> Dear all,
> > >>
> > >> Is it possible to obtain skewness and kurtosis summary measures from
> > MINC
> > >> volumes? As far as I could see, mincstats does not offer this option.
> > >>
> > >> Thanks,
> > >> Pedro
> > >> _______________________________________________
> > >> 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 gdevenyi at gmail.com  Thu Aug  6 13:04:50 2015
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Thu, 6 Aug 2015 13:04:50 -0400
Subject: [MINC-users] Display.globals options was: Re: Visualizing data
 with high dynamic range
In-Reply-To: <CAAd5DeTMVh3nHO+L-WFGR0pkQKPbbwYDWpVy=qUS3-Z5fQvAjg@mail.gmail.com>
References: <CAFQOoOpZAqRu+NShxjTnNMK+wj3q9+r=r51hcqqbhqy0sJ5njA@mail.gmail.com>
	<CAAd5DeTMVh3nHO+L-WFGR0pkQKPbbwYDWpVy=qUS3-Z5fQvAjg@mail.gmail.com>
Message-ID: <CAFQOoOpVDHGk+oO=oV-Y4JmPcy-iCNN_MsBUiSNZDD6qu8qBeA@mail.gmail.com>

Thanks Bert!
On Aug 6, 2015 12:55, "Robert D. Vincent" <robert.d.vincent at mcgill.ca>
wrote:

> Hi Gabriel,
>
> There's no real documentation on this. There has been some recent work on
> improving the Display manual, which I hope to release sometime in the next
> few months. I'll make it a point to add documentation of some of the more
> "interesting" globals.
>
>     -bert
>
> On Wed, Aug 5, 2015 at 4:42 PM, Gabriel A. Devenyi <gdevenyi at gmail.com>
> wrote:
>
> > Bert,
> >
> > Are there docs somewhere on what we can specify for Display.globals?
> >
> > --
> > Gabriel A. Devenyi B.Eng. Ph.D.
> > Research Computing Associate
> > Computational Brain Anatomy Laboratory
> > Cerebral Imaging Center
> > Douglas Mental Health University Institute
> > McGill University
> > t: 514.761.6131x4781
> > e: gdevenyi at gmail.com
> >
> > On Wed, Aug 5, 2015 at 10:45 AM, Robert D. Vincent <
> > robert.d.vincent at mcgill.ca> wrote:
> >
> > > Hi Andrew,
> > >
> > > Display should be able to handle high dynamic range data. There is a
> > global
> > > variable "Convert_volumes_to_byte" which is true by default, but which
> > can
> > > be overridden either on the command line or the Display.globals
> > > initialization file. You can set it either by specifying:
> > >
> > > Display -global Convert_volumes_to_byte false <input.mnc>
> > >
> > > or by adding the line:
> > >
> > > Convert_volumes_to_byte=False;
> > >
> > > to a file named Display.globals in your home directory.
> > >
> > > Register has similar functionality, but it was added fairly recently,
> so
> > I
> > > don't believe it is widely available. The code checked into Github
> > supports
> > > two globals, Volume_voxel_type and Volume_voxel_signed, that control
> the
> > > conversion of loaded volumes.
> > >
> > > Hope this helps. I intend to change the default behavior in future
> > versions
> > > of Display, but I haven't made the change yet.
> > >
> > >     -bert
> > >
> > > On Wed, Aug 5, 2015 at 9:41 AM, Andrew Wood <andrew at biospective.com>
> > > wrote:
> > >
> > > > Hi all,
> > > >
> > > > I'm having trouble visualizing a volume containing float data with a
> > high
> > > > dynamic range. Both register and Display discretize the signal (down
> to
> > > > byte precision?), which is not workable for these volumes.
> > > >
> > > > The only solution I have right now is to explode the data into new
> > > volumes
> > > > by sliding a reduced range over the signal, clamping away data that
> > > > register and Display can't handle.
> > > >
> > > > Does anyone have experience visualizing high dynamic range data? Is
> > > there a
> > > > tool that can do this, or just a better workaround?
> > > >
> > > > 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
> >
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From a.janke at gmail.com  Sun Aug  9 22:28:02 2015
From: a.janke at gmail.com (Andrew Janke)
Date: Mon, 10 Aug 2015 12:28:02 +1000
Subject: [MINC-users] CPU Speed
Message-ID: <CAG0CB22d=XwdZHuz1gDqQbD0JpKAh2=NJjxccv5wVELrD7SBew@mail.gmail.com>

Anyone elase find it somewhat annoying that things haven't really got
all that faster in CPU's over the last few years. New desktop Xeon
based Dell (Precision 5810) is about 14seconds faster than the 6 year
old i7-950 it replaced. See the last line here:

   https://en.wikibooks.org/wiki/MINC/Benchmarks

We have more cores available for the same $$ spent, but they aren't
getting much faster. They are however available in laptops. Either
that or a 10% change is not impressive anymore. To put it all in
perspective, a 2mm non-linear fit that used to take Louis about an
hour when he wrote minctracc now takes just under 2 minutes.


a

From zijdenbos at gmail.com  Sun Aug  9 22:52:52 2015
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Sun, 9 Aug 2015 22:52:52 -0400
Subject: [MINC-users] CPU Speed
In-Reply-To: <CAG0CB22d=XwdZHuz1gDqQbD0JpKAh2=NJjxccv5wVELrD7SBew@mail.gmail.com>
References: <CAG0CB22d=XwdZHuz1gDqQbD0JpKAh2=NJjxccv5wVELrD7SBew@mail.gmail.com>
Message-ID: <CABEEk14qow_afOq2GgzQ-8u0o4+ZEhya5K3fy7FN0A9h6Uv6Gg@mail.gmail.com>

Yeah CPU speed increase definitely seems to be leveling off. There are some
hardware reasons for that of course (heat dissipation seems to be one of
the main issues,
http://electronics.stackexchange.com/questions/122050/what-limits-cpu-speed
).

But is the MINC benchmark perhaps not so valid anymore - at under 2 mins of
any MINC process, wouldn't the brunt of that time be spent on I/O, not
computation?

But yes, there's the increasing number of cores that do provide more
cycles, not counted in single-thread processes. Perhaps we should have
benchmarked with respect to $$ instead of time :-)

-- A

On Sun, Aug 9, 2015 at 10:28 PM, Andrew Janke <a.janke at gmail.com> wrote:

> Anyone elase find it somewhat annoying that things haven't really got
> all that faster in CPU's over the last few years. New desktop Xeon
> based Dell (Precision 5810) is about 14seconds faster than the 6 year
> old i7-950 it replaced. See the last line here:
>
>    https://en.wikibooks.org/wiki/MINC/Benchmarks
>
> We have more cores available for the same $$ spent, but they aren't
> getting much faster. They are however available in laptops. Either
> that or a 10% change is not impressive anymore. To put it all in
> perspective, a 2mm non-linear fit that used to take Louis about an
> hour when he wrote minctracc now takes just under 2 minutes.
>
>
> a
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>

From pierre.bellec at criugm.qc.ca  Sun Aug  9 22:57:00 2015
From: pierre.bellec at criugm.qc.ca (Pierre Bellec)
Date: Sun, 9 Aug 2015 22:57:00 -0400
Subject: [MINC-users] CPU Speed
In-Reply-To: <CAG0CB22d=XwdZHuz1gDqQbD0JpKAh2=NJjxccv5wVELrD7SBew@mail.gmail.com>
References: <CAG0CB22d=XwdZHuz1gDqQbD0JpKAh2=NJjxccv5wVELrD7SBew@mail.gmail.com>
Message-ID: <CADPHwxCa8si+84WqrJpyW-uKd+C0mbmYkVFay2EdEOLAKT7XQQ@mail.gmail.com>

Very nice benchmark Andrew! As Alex said, the number of threads has
increased quite a bit in addition to pure single-thread speed, which is
hard to factor in a benchmark. Looks like GPUs are the way to reduce
dramatically computations for single datasets, e.g. BROCCOLI
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3953750/ "non-linear spatial
normalization to a 1 mm3 brain template in 4?6 s" Not sure this includes
I/O though.

Best,

Pierre

Pierre Bellec
http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec
Telephone              (1) 514 713 5596
SIMEXP lab            http://simexp-lab.org

On Sun, Aug 9, 2015 at 10:28 PM, Andrew Janke <a.janke at gmail.com> wrote:

> Anyone elase find it somewhat annoying that things haven't really got
> all that faster in CPU's over the last few years. New desktop Xeon
> based Dell (Precision 5810) is about 14seconds faster than the 6 year
> old i7-950 it replaced. See the last line here:
>
>    https://en.wikibooks.org/wiki/MINC/Benchmarks
>
> We have more cores available for the same $$ spent, but they aren't
> getting much faster. They are however available in laptops. Either
> that or a 10% change is not impressive anymore. To put it all in
> perspective, a 2mm non-linear fit that used to take Louis about an
> hour when he wrote minctracc now takes just under 2 minutes.
>
>
> a
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From vladimir.fonov at gmail.com  Mon Aug 10 11:11:44 2015
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Mon, 10 Aug 2015 11:11:44 -0400
Subject: [MINC-users] CPU Speed
In-Reply-To: <CAG0CB22d=XwdZHuz1gDqQbD0JpKAh2=NJjxccv5wVELrD7SBew@mail.gmail.com>
References: <CAG0CB22d=XwdZHuz1gDqQbD0JpKAh2=NJjxccv5wVELrD7SBew@mail.gmail.com>
Message-ID: <55C8BF30.1020404@gmail.com>

Time to adapt openMP in mni_autoreg!

On 15-08-09 10:28 PM, Andrew Janke wrote:
> Anyone elase find it somewhat annoying that things haven't really got
> all that faster in CPU's over the last few years. New desktop Xeon
> based Dell (Precision 5810) is about 14seconds faster than the 6 year
> old i7-950 it replaced. See the last line here:
>
>     https://en.wikibooks.org/wiki/MINC/Benchmarks
>
> We have more cores available for the same $$ spent, but they aren't
> getting much faster. They are however available in laptops. Either
> that or a 10% change is not impressive anymore. To put it all in
> perspective, a 2mm non-linear fit that used to take Louis about an
> hour when he wrote minctracc now takes just under 2 minutes.

-- 
Best regards,

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

From gdevenyi at gmail.com  Fri Aug 14 14:32:10 2015
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Fri, 14 Aug 2015 14:32:10 -0400
Subject: [MINC-users] Visually distinct colour map for Display labels
Message-ID: <CAFQOoOp7syWLzZzr_CciVV8vLXQ_PPAkeerKY2J1C6dp=Jh+Vg@mail.gmail.com>

Hi all,

I was having trouble with Display choosing colours that were too close to
each other for some adjacent labels, so I decided to fix it. I produced a
colormap using http://tools.medialab.sciences-po.fr/iwanthue/index.php with
256 distinct colours with high lightness and formatted it for Display.

You can download a copy here:
http://cobralab.net/files/distinct-labels.map

To use it either load with "File -> Load Color Map" or supply as an input
file on your command line-call.

Thanks to Robert Vincent for helping me find how to load custom label
colour maps.

-- 
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
McGill University
t: 514.761.6131x4781
e: gdevenyi at gmail.com

From robert.d.vincent at mcgill.ca  Sat Aug 15 09:40:24 2015
From: robert.d.vincent at mcgill.ca (Robert D. Vincent)
Date: Sat, 15 Aug 2015 09:40:24 -0400
Subject: [MINC-users] Visually distinct colour map for Display labels
In-Reply-To: <CAFQOoOp7syWLzZzr_CciVV8vLXQ_PPAkeerKY2J1C6dp=Jh+Vg@mail.gmail.com>
References: <CAFQOoOp7syWLzZzr_CciVV8vLXQ_PPAkeerKY2J1C6dp=Jh+Vg@mail.gmail.com>
Message-ID: <CAAd5DeQSXmxbanHAzey11z4=aa38ZCf_ojP6a4qGDmnEtnAr3g@mail.gmail.com>

Hi Gabriel,

Would you have any objection to our incorporating this as an option in
future versions of Display?

    -bert

On Fri, Aug 14, 2015 at 2:32 PM, Gabriel A. Devenyi <gdevenyi at gmail.com>
wrote:

> Hi all,
>
> I was having trouble with Display choosing colours that were too close to
> each other for some adjacent labels, so I decided to fix it. I produced a
> colormap using http://tools.medialab.sciences-po.fr/iwanthue/index.php
> with
> 256 distinct colours with high lightness and formatted it for Display.
>
> You can download a copy here:
> http://cobralab.net/files/distinct-labels.map
>
> To use it either load with "File -> Load Color Map" or supply as an input
> file on your command line-call.
>
> Thanks to Robert Vincent for helping me find how to load custom label
> colour maps.
>
> --
> Gabriel A. Devenyi B.Eng. Ph.D.
> Research Computing Associate
> Computational Brain Anatomy Laboratory
> Cerebral Imaging Center
> Douglas Mental Health University Institute
> McGill University
> t: 514.761.6131x4781
> e: gdevenyi at gmail.com
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From gdevenyi at gmail.com  Sat Aug 15 10:03:52 2015
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Sat, 15 Aug 2015 10:03:52 -0400
Subject: [MINC-users] Visually distinct colour map for Display labels
In-Reply-To: <CAAd5DeQSXmxbanHAzey11z4=aa38ZCf_ojP6a4qGDmnEtnAr3g@mail.gmail.com>
References: <CAFQOoOp7syWLzZzr_CciVV8vLXQ_PPAkeerKY2J1C6dp=Jh+Vg@mail.gmail.com>
	<CAAd5DeQSXmxbanHAzey11z4=aa38ZCf_ojP6a4qGDmnEtnAr3g@mail.gmail.com>
Message-ID: <CAFQOoOoSkhMjLbGt9DHnRhJK7zQqXHUf=bAr16c0S9QjZdFy7w@mail.gmail.com>

Please do!
On Aug 15, 2015 9:41 AM, "Robert D. Vincent" <robert.d.vincent at mcgill.ca>
wrote:

> Hi Gabriel,
>
> Would you have any objection to our incorporating this as an option in
> future versions of Display?
>
>     -bert
>
> On Fri, Aug 14, 2015 at 2:32 PM, Gabriel A. Devenyi <gdevenyi at gmail.com>
> wrote:
>
> > Hi all,
> >
> > I was having trouble with Display choosing colours that were too close to
> > each other for some adjacent labels, so I decided to fix it. I produced a
> > colormap using http://tools.medialab.sciences-po.fr/iwanthue/index.php
> > with
> > 256 distinct colours with high lightness and formatted it for Display.
> >
> > You can download a copy here:
> > http://cobralab.net/files/distinct-labels.map
> >
> > To use it either load with "File -> Load Color Map" or supply as an input
> > file on your command line-call.
> >
> > Thanks to Robert Vincent for helping me find how to load custom label
> > colour maps.
> >
> > --
> > Gabriel A. Devenyi B.Eng. Ph.D.
> > Research Computing Associate
> > Computational Brain Anatomy Laboratory
> > Cerebral Imaging Center
> > Douglas Mental Health University Institute
> > McGill University
> > t: 514.761.6131x4781
> > e: gdevenyi at gmail.com
> > _______________________________________________
> > 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 cfederau at stanford.edu  Sat Aug 22 16:17:19 2015
From: cfederau at stanford.edu (Christian Emil Federau)
Date: Sat, 22 Aug 2015 20:17:19 +0000
Subject: [MINC-users] zoom in register using a mac mighty mouse.
Message-ID: <0FB17D67-65A6-4D69-A9A5-D5387AF715F7@stanford.edu>

Hi all, 

I am looking for a way to zoom in register using a mac mighty mouse. It is the middle button on a mouse with three buttons. Has anyone solved this problem? 

thanks a lot,

Christian 



From robert.d.vincent at mcgill.ca  Sun Aug 23 08:26:23 2015
From: robert.d.vincent at mcgill.ca (Robert D. Vincent)
Date: Sun, 23 Aug 2015 08:26:23 -0400
Subject: [MINC-users] zoom in register using a mac mighty mouse.
In-Reply-To: <0FB17D67-65A6-4D69-A9A5-D5387AF715F7@stanford.edu>
References: <0FB17D67-65A6-4D69-A9A5-D5387AF715F7@stanford.edu>
Message-ID: <CAAd5DeS34LmCCDt3JcPHSHW=ityWzN=qw+VM1f0RzaXOSj+P7g@mail.gmail.com>

Hi Christian,

I have added scroll support (via mouse wheel or trackpad) for zooming to
the "register" and "Display" code. I believe this should have made it into
release 1.9.10 of the minc-toolkit, available here:

http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit

If this doesn't fix the issue, let me know, and we may be able to find
another workaround.

    -bert

On Sat, Aug 22, 2015 at 4:17 PM, Christian Emil Federau <
cfederau at stanford.edu> wrote:

> Hi all,
>
> I am looking for a way to zoom in register using a mac mighty mouse. It is
> the middle button on a mouse with three buttons. Has anyone solved this
> problem?
>
> thanks a lot,
>
> Christian
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From trash001 at odu.edu  Sun Aug 23 21:34:48 2015
From: trash001 at odu.edu (TANWEER RASHID)
Date: Sun, 23 Aug 2015 21:34:48 -0400
Subject: [MINC-users] Padding for minc volumes
Message-ID: <CAE1j2uhv7mbMEY=j786=J3vCmt+WHehx6H3sUN3bGqXnXx6+Rg@mail.gmail.com>

Hi,

Is there any way to add a layer of padding to an existing minc file. I am
trying to create a 1 or 2 voxel layer of padding around the edges of the
volume.

Thanks,
-- 
Tanweer Rashid
MSVE Dept.
Old Dominion University

From zijdenbos at gmail.com  Sun Aug 23 22:00:03 2015
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Sun, 23 Aug 2015 22:00:03 -0400
Subject: [MINC-users] Padding for minc volumes
In-Reply-To: <CAE1j2uhv7mbMEY=j786=J3vCmt+WHehx6H3sUN3bGqXnXx6+Rg@mail.gmail.com>
References: <CAE1j2uhv7mbMEY=j786=J3vCmt+WHehx6H3sUN3bGqXnXx6+Rg@mail.gmail.com>
Message-ID: <CABEEk16ZAiJUwm_CcnUtRDcS2JUNgm_OubMsqdWVGOKdMKxZEg@mail.gmail.com>

Hi Tanweer,

Yes - autcrop will do that for you:

autocrop -isoexpand 1v <in.mnc> <out.mnc>

for a 1-voxel padding all around.

autocrop calls mincreshape or mincresample; you can also use mincreshape
directly, but in that case you will need to calculate the arguments to
-start and -count yourself.

-- A


On Sun, Aug 23, 2015 at 9:34 PM, TANWEER RASHID <trash001 at odu.edu> wrote:

> Hi,
>
> Is there any way to add a layer of padding to an existing minc file. I am
> trying to create a 1 or 2 voxel layer of padding around the edges of the
> volume.
>
> Thanks,
> --
> Tanweer Rashid
> MSVE Dept.
> Old Dominion University
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>

From Oury.Monchi at ucalgary.ca  Wed Aug 26 17:14:39 2015
From: Oury.Monchi at ucalgary.ca (Oury Monchi)
Date: Wed, 26 Aug 2015 21:14:39 +0000
Subject: [MINC-users] dcm2mnc GE 3T
Message-ID: <D203885D.1F085%oury.monchi@ucalgary.ca>

Dear all,

I am trying to find out if there is a version of dcm2mnc that has been tried on dicom files from a GE 3T scanner.

Best,
Oury.

Oury Monchi, PhD

Professor and Tourmaline Chair in Parkinson?s Disease

Departments of Clinical Neurosciences and Radiology,
Leader of the Movement Disorders Research Neuroteam,

Director of Clinical Research,

Hotchkiss Brain Institute,

Cumming School of Medicine, University of Calgary.
Tel: 403-2208048
E-mail:oury.monchi at ucalgary.ca
http://pcanlab.ca/



From gdevenyi at gmail.com  Wed Aug 26 19:10:13 2015
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Wed, 26 Aug 2015 19:10:13 -0400
Subject: [MINC-users] HOWTO: building and installing brain-view2 on Ubuntu
	14.04.3
Message-ID: <CAFQOoOrg-sK8VpoeYXMTPoTJVFCZ3O5AWrJCsv_e513HKfhWGg@mail.gmail.com>

Hi all,

Since I?ve had many collaborators who?ve recently wanted to start using
brain-view2 and found that it?s nearly impossible to install, I have
documented a minimal set of steps to install brain-view2 on a *fresh*
install of Ubuntu 14.04.3. This script makes no attempts to check anything.
Hopefully you can adapt this to your own needs based on your system:

This is designed to be run as root, so do sudo -i before running the script

#!/bin/bashset -e
apt-get update
apt-get install -y build-essential gdebi-core git libcoin80-dev
qt4-qmake libqt4-dev libqt4-core libboost-dev autogen pkg-config
libtool libpcre++-dev gdb
cd ~
wget http://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/minc-toolkit-1.9.10-20150710-Ubuntu_14.04-x86_64.deb

gdebi -n ~/minc-toolkit-1.9.10-20150710-Ubuntu_14.04-x86_64.deb
source /opt/minc-itk4/minc-toolkit-config.sh
#brain-view2 mess
mkdir ~/brain-view-buildcd ~/brain-view-build
#Install Quarter#Original source of Quarter is dead...
wget https://distfiles.macports.org/Quarter/Quarter-1.0.0.tar.gz

tar -xzf Quarter-1.0.0.tar.gzcd ~/brain-view-build/Quarter-1.0.0 &&
./configure && make && make install
#Install bicInventor#Cloning my patched version of bicInventor until
pull-request to MNI version is integrated
git clone https://github.com/gdevenyi/bicInventor.git
cd ~/brain-view-build/bicInventor && ./autogen.sh && ./configure
--prefix=/opt/minc-itk4 --with-build-path=/opt/minc-itk4 --with-minc2
&& make && make install
#Install brain-view2
git clone https://github.com/sghanavati/brain-view2.gitcd
~/brain-view-build/brain-view2 && qmake MINCDIR=/opt/minc-itk4
HDF5DIR=/opt/minc-itk4 && make && cp brain-view2 /opt/minc-itk4/bin

?
-- 
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
McGill University
t: 514.761.6131x4781
e: gdevenyi at gmail.com

From gdevenyi at gmail.com  Wed Aug 26 19:34:47 2015
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Wed, 26 Aug 2015 19:34:47 -0400
Subject: [MINC-users] HOWTO: building and installing brain-view2 on
	Ubuntu 14.04.3
In-Reply-To: <CAFQOoOrg-sK8VpoeYXMTPoTJVFCZ3O5AWrJCsv_e513HKfhWGg@mail.gmail.com>
References: <CAFQOoOrg-sK8VpoeYXMTPoTJVFCZ3O5AWrJCsv_e513HKfhWGg@mail.gmail.com>
Message-ID: <CAFQOoOoKowF2a8p7cHEXQGcByh70rdC_GRQH_SU9B-b=vyHGJA@mail.gmail.com>

And I made some mistakes cleaning up my script with copy/paste, sorry!

#!/bin/bashset -e
apt-get update
apt-get install -y build-essential gdebi-core git libcoin80-dev
qt4-qmake libqt4-dev libqt4-core libboost-dev autogen pkg-config
libtool libpcre++-dev gdb automake
cd ~
wget http://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/minc-toolkit-1.9.10-20150710-Ubuntu_14.04-x86_64.deb

gdebi -n ~/minc-toolkit-1.9.10-20150710-Ubuntu_14.04-x86_64.deb
source /opt/minc-itk4/minc-toolkit-config.sh
#brain-view2 mess
mkdir ~/brain-view-buildcd ~/brain-view-build
#Install Quarter#Original source of Quarter is dead...
wget https://distfiles.macports.org/Quarter/Quarter-1.0.0.tar.gz

tar -xzf Quarter-1.0.0.tar.gzcd ~/brain-view-build/Quarter-1.0.0 &&
./configure --prefix=/opt/minc-itk4 && make && make install
#Install bicInventorcd ~/brain-view-build
#Cloning my patched version of bicInventor until pull-request to MNI
version is integrated
git clone https://github.com/gdevenyi/bicInventor.git
cd ~/brain-view-build/bicInventor && ./autogen.sh && ./configure
--prefix=/opt/minc-itk4 --with-build-path=/opt/minc-itk4 --with-minc2
&& make && make install
#Install brain-view2cd ~/brain-view-build

git clone https://github.com/sghanavati/brain-view2.gitcd
~/brain-view-build/brain-view2 && qmake MINCDIR=/opt/minc-itk4
HDF5DIR=/opt/minc-itk4 INVENTORDIR=/opt/minc-itk4
QUARTERDIR=/opt/minc-itk4   && make && cp brain-view2
/opt/minc-itk4/bin

?

-- 
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
McGill University
t: 514.761.6131x4781
e: gdevenyi at gmail.com

On Wed, Aug 26, 2015 at 7:10 PM, Gabriel A. Devenyi <gdevenyi at gmail.com>
wrote:

> Hi all,
>
> Since I?ve had many collaborators who?ve recently wanted to start using
> brain-view2 and found that it?s nearly impossible to install, I have
> documented a minimal set of steps to install brain-view2 on a *fresh*
> install of Ubuntu 14.04.3. This script makes no attempts to check anything.
> Hopefully you can adapt this to your own needs based on your system:
>
> This is designed to be run as root, so do sudo -i before running the
> script
>
> #!/bin/bashset -e
> apt-get update
> apt-get install -y build-essential gdebi-core git libcoin80-dev qt4-qmake libqt4-dev libqt4-core libboost-dev autogen pkg-config libtool libpcre++-dev gdb
> cd ~
> wget http://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/minc-toolkit-1.9.10-20150710-Ubuntu_14.04-x86_64.deb
>
> gdebi -n ~/minc-toolkit-1.9.10-20150710-Ubuntu_14.04-x86_64.deb
> source /opt/minc-itk4/minc-toolkit-config.sh
> #brain-view2 mess
> mkdir ~/brain-view-buildcd ~/brain-view-build
> #Install Quarter#Original source of Quarter is dead...
> wget https://distfiles.macports.org/Quarter/Quarter-1.0.0.tar.gz
>
> tar -xzf Quarter-1.0.0.tar.gzcd ~/brain-view-build/Quarter-1.0.0 && ./configure && make && make install
> #Install bicInventor#Cloning my patched version of bicInventor until pull-request to MNI version is integrated
> git clone https://github.com/gdevenyi/bicInventor.git
> cd ~/brain-view-build/bicInventor && ./autogen.sh && ./configure --prefix=/opt/minc-itk4 --with-build-path=/opt/minc-itk4 --with-minc2 && make && make install
> #Install brain-view2
> git clone https://github.com/sghanavati/brain-view2.gitcd ~/brain-view-build/brain-view2 && qmake MINCDIR=/opt/minc-itk4 HDF5DIR=/opt/minc-itk4 && make && cp brain-view2 /opt/minc-itk4/bin
>
> ?
> --
> Gabriel A. Devenyi B.Eng. Ph.D.
> Research Computing Associate
> Computational Brain Anatomy Laboratory
> Cerebral Imaging Center
> Douglas Mental Health University Institute
> McGill University
> t: 514.761.6131x4781
> e: gdevenyi at gmail.com
>

From jon at pipitone.ca  Wed Aug 26 19:47:52 2015
From: jon at pipitone.ca (Jon Pipitone)
Date: Wed, 26 Aug 2015 19:47:52 -0400
Subject: [MINC-users] dcm2mnc GE 3T
Message-ID: <20150826235252.6C2F4318095@homiemail-a89.g.dreamhost.com>

Hi,

We use dcm2mnc from minc-toolkit v1.0.01 on GE 3T scans all the time.

Are you encountering problems?

Jon.

On Aug 26, 2015 5:14 PM, Oury Monchi <Oury.Monchi at ucalgary.ca> wrote:
>
> Dear all, 
>
> I am trying to find out if there is a version of dcm2mnc that has been tried on dicom files from a GE 3T scanner. 
>
> Best, 
> Oury. 
>
> Oury Monchi, PhD 
>
> Professor and Tourmaline Chair in Parkinson?s Disease 
>
> Departments of Clinical Neurosciences and Radiology, 
> Leader of the Movement Disorders Research Neuroteam, 
>
> Director of Clinical Research, 
>
> Hotchkiss Brain Institute, 
>
> Cumming School of Medicine, University of Calgary. 
> Tel: 403-2208048 
> E-mail:oury.monchi at ucalgary.ca 
> http://pcanlab.ca/ 
>
>
> _______________________________________________ 
> MINC-users at bic.mni.mcgill.ca 
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users 

From Oury.Monchi at ucalgary.ca  Wed Aug 26 19:57:59 2015
From: Oury.Monchi at ucalgary.ca (Oury Monchi)
Date: Wed, 26 Aug 2015 23:57:59 +0000
Subject: [MINC-users] dcm2mnc GE 3T
In-Reply-To: <20150826235252.6C2F4318095@homiemail-a89.g.dreamhost.com>
References: <20150826235252.6C2F4318095@homiemail-a89.g.dreamhost.com>
Message-ID: <5C8B702FE8D56248BE43D5CF0C69732D2BDB1327@ITCIMEXCH04.uc.ucalgary.ca>

We have tried with v2 and had problems with 4d data Bold and DTI.

Will try with v1 .

Thank you,
Oury.

Sent from my HTC

----- Reply message -----
From: "Jon Pipitone" <jon at pipitone.ca>
To: "MINC users mailing list" <minc-users at bic.mni.mcgill.ca>
Subject: [MINC-users] dcm2mnc GE 3T
Date: Wed, Aug 26, 2015 5:54 PM

Hi,

We use dcm2mnc from minc-toolkit v1.0.01 on GE 3T scans all the time.

Are you encountering problems?

Jon.

On Aug 26, 2015 5:14 PM, Oury Monchi <Oury.Monchi at ucalgary.ca> wrote:
>
> Dear all,
>
> I am trying to find out if there is a version of dcm2mnc that has been tried on dicom files from a GE 3T scanner.
>
> Best,
> Oury.
>
> Oury Monchi, PhD
>
> Professor and Tourmaline Chair in Parkinson?s Disease
>
> Departments of Clinical Neurosciences and Radiology,
> Leader of the Movement Disorders Research Neuroteam,
>
> Director of Clinical Research,
>
> Hotchkiss Brain Institute,
>
> Cumming School of Medicine, University of Calgary.
> Tel: 403-2208048
> E-mail:oury.monchi at ucalgary.ca
> http://pcanlab.ca/
>
>
> _______________________________________________
> 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 gdevenyi at gmail.com  Wed Aug 26 20:02:54 2015
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Wed, 26 Aug 2015 20:02:54 -0400
Subject: [MINC-users] HOWTO: building and installing brain-view2 on
	Ubuntu 14.04.3
In-Reply-To: <CAFQOoOoKowF2a8p7cHEXQGcByh70rdC_GRQH_SU9B-b=vyHGJA@mail.gmail.com>
References: <CAFQOoOrg-sK8VpoeYXMTPoTJVFCZ3O5AWrJCsv_e513HKfhWGg@mail.gmail.com>
	<CAFQOoOoKowF2a8p7cHEXQGcByh70rdC_GRQH_SU9B-b=vyHGJA@mail.gmail.com>
Message-ID: <CAFQOoOo9KAMivmfDsJ3Ti3-TrKkyPoCan=hkTH2LEdXXRj+Rbg@mail.gmail.com>

And once more with feeling, it seems the mailing list mangled the line
lengths:

https://gist.github.com/gdevenyi/df0f1f6c589b2b8f9481

-- 
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
McGill University
t: 514.761.6131x4781
e: gdevenyi at gmail.com

On Wed, Aug 26, 2015 at 7:34 PM, Gabriel A. Devenyi <gdevenyi at gmail.com>
wrote:

> And I made some mistakes cleaning up my script with copy/paste, sorry!
>
> #!/bin/bashset -e
> apt-get update
> apt-get install -y build-essential gdebi-core git libcoin80-dev qt4-qmake libqt4-dev libqt4-core libboost-dev autogen pkg-config libtool libpcre++-dev gdb automake
> cd ~
> wget http://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/minc-toolkit-1.9.10-20150710-Ubuntu_14.04-x86_64.deb
>
> gdebi -n ~/minc-toolkit-1.9.10-20150710-Ubuntu_14.04-x86_64.deb
> source /opt/minc-itk4/minc-toolkit-config.sh
> #brain-view2 mess
> mkdir ~/brain-view-buildcd ~/brain-view-build
> #Install Quarter#Original source of Quarter is dead...
> wget https://distfiles.macports.org/Quarter/Quarter-1.0.0.tar.gz
>
> tar -xzf Quarter-1.0.0.tar.gzcd ~/brain-view-build/Quarter-1.0.0 && ./configure --prefix=/opt/minc-itk4 && make && make install
> #Install bicInventorcd ~/brain-view-build
> #Cloning my patched version of bicInventor until pull-request to MNI version is integrated
> git clone https://github.com/gdevenyi/bicInventor.git
> cd ~/brain-view-build/bicInventor && ./autogen.sh && ./configure --prefix=/opt/minc-itk4 --with-build-path=/opt/minc-itk4 --with-minc2 && make && make install
> #Install brain-view2cd ~/brain-view-build
>
> git clone https://github.com/sghanavati/brain-view2.gitcd ~/brain-view-build/brain-view2 && qmake MINCDIR=/opt/minc-itk4 HDF5DIR=/opt/minc-itk4 INVENTORDIR=/opt/minc-itk4 QUARTERDIR=/opt/minc-itk4   && make && cp brain-view2 /opt/minc-itk4/bin
>
> ?
>
> --
> Gabriel A. Devenyi B.Eng. Ph.D.
> Research Computing Associate
> Computational Brain Anatomy Laboratory
> Cerebral Imaging Center
> Douglas Mental Health University Institute
> McGill University
> t: 514.761.6131x4781
> e: gdevenyi at gmail.com
>
> On Wed, Aug 26, 2015 at 7:10 PM, Gabriel A. Devenyi <gdevenyi at gmail.com>
> wrote:
>
>> Hi all,
>>
>> Since I?ve had many collaborators who?ve recently wanted to start using
>> brain-view2 and found that it?s nearly impossible to install, I have
>> documented a minimal set of steps to install brain-view2 on a *fresh*
>> install of Ubuntu 14.04.3. This script makes no attempts to check anything.
>> Hopefully you can adapt this to your own needs based on your system:
>>
>> This is designed to be run as root, so do sudo -i before running the
>> script
>>
>> #!/bin/bashset -e
>> apt-get update
>> apt-get install -y build-essential gdebi-core git libcoin80-dev qt4-qmake libqt4-dev libqt4-core libboost-dev autogen pkg-config libtool libpcre++-dev gdb
>> cd ~
>> wget http://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/minc-toolkit-1.9.10-20150710-Ubuntu_14.04-x86_64.deb
>>
>> gdebi -n ~/minc-toolkit-1.9.10-20150710-Ubuntu_14.04-x86_64.deb
>> source /opt/minc-itk4/minc-toolkit-config.sh
>> #brain-view2 mess
>> mkdir ~/brain-view-buildcd ~/brain-view-build
>> #Install Quarter#Original source of Quarter is dead...
>> wget https://distfiles.macports.org/Quarter/Quarter-1.0.0.tar.gz
>>
>> tar -xzf Quarter-1.0.0.tar.gzcd ~/brain-view-build/Quarter-1.0.0 && ./configure && make && make install
>> #Install bicInventor#Cloning my patched version of bicInventor until pull-request to MNI version is integrated
>> git clone https://github.com/gdevenyi/bicInventor.git
>> cd ~/brain-view-build/bicInventor && ./autogen.sh && ./configure --prefix=/opt/minc-itk4 --with-build-path=/opt/minc-itk4 --with-minc2 && make && make install
>> #Install brain-view2
>> git clone https://github.com/sghanavati/brain-view2.gitcd ~/brain-view-build/brain-view2 && qmake MINCDIR=/opt/minc-itk4 HDF5DIR=/opt/minc-itk4 && make && cp brain-view2 /opt/minc-itk4/bin
>>
>> ?
>> --
>> Gabriel A. Devenyi B.Eng. Ph.D.
>> Research Computing Associate
>> Computational Brain Anatomy Laboratory
>> Cerebral Imaging Center
>> Douglas Mental Health University Institute
>> McGill University
>> t: 514.761.6131x4781
>> e: gdevenyi at gmail.com
>>
>
>

From jon at pipitone.ca  Wed Aug 26 20:05:34 2015
From: jon at pipitone.ca (jon at pipitone.ca)
Date: Thu, 27 Aug 2015 00:05:34 +0000
Subject: [MINC-users] dcm2mnc GE 3T
In-Reply-To: <5C8B702FE8D56248BE43D5CF0C69732D2BDB1327@ITCIMEXCH04.uc.ucalgary.ca>
References: <5C8B702FE8D56248BE43D5CF0C69732D2BDB1327@ITCIMEXCH04.uc.ucalgary.ca>
	<20150826235252.6C2F4318095@homiemail-a89.g.dreamhost.com>
Message-ID: <41d5a465c705b1b8a9240f669fef995f@jon.pipitone.ca>

Ah, can't speak to 4D data with dcm2mnc as we use nifti-based tools for those. 

Jon. 

August 26 2015 7:59 PM, "Oury Monchi" <oury.monchi at ucalgary.ca> wrote:
> We have tried with v2 and had problems with 4d data Bold and DTI.
> 
> Will try with v1 .
> 
> Thank you,
> Oury.
> 
> Sent from my HTC
> 
> ----- Reply message -----
> From: "Jon Pipitone" <jon at pipitone.ca>
> To: "MINC users mailing list" <minc-users at bic.mni.mcgill.ca>
> Subject: [MINC-users] dcm2mnc GE 3T
> Date: Wed, Aug 26, 2015 5:54 PM
> 
> Hi,
> 
> We use dcm2mnc from minc-toolkit v1.0.01 on GE 3T scans all the time.
> 
> Are you encountering problems?
> 
> Jon.
> 
> On Aug 26, 2015 5:14 PM, Oury Monchi <Oury.Monchi at ucalgary.ca> wrote:
> 
>> Dear all,
>> 
>> I am trying to find out if there is a version of dcm2mnc that has been tried on dicom files from a
>> GE 3T scanner.
>> 
>> Best,
>> Oury.
>> 
>> Oury Monchi, PhD
>> 
>> Professor and Tourmaline Chair in Parkinson?s Disease
>> 
>> Departments of Clinical Neurosciences and Radiology,
>> Leader of the Movement Disorders Research Neuroteam,
>> 
>> Director of Clinical Research,
>> 
>> Hotchkiss Brain Institute,
>> 
>> Cumming School of Medicine, University of Calgary.
>> Tel: 403-2208048
>> E-mail:oury.monchi at ucalgary.ca
>> http://pcanlab.ca
>> 
>> _______________________________________________
>> 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 robert.d.vincent at mcgill.ca  Wed Aug 26 20:36:36 2015
From: robert.d.vincent at mcgill.ca (Robert D. Vincent)
Date: Wed, 26 Aug 2015 20:36:36 -0400
Subject: [MINC-users] dcm2mnc GE 3T
In-Reply-To: <5C8B702FE8D56248BE43D5CF0C69732D2BDB1327@ITCIMEXCH04.uc.ucalgary.ca>
References: <20150826235252.6C2F4318095@homiemail-a89.g.dreamhost.com>
	<5C8B702FE8D56248BE43D5CF0C69732D2BDB1327@ITCIMEXCH04.uc.ucalgary.ca>
Message-ID: <CAAd5DeRWTne8O7qEGyPqkVyXA8=SfqiNnSAbcx6S+7PJYL+r_w@mail.gmail.com>

Hi Oury,

We have made quite a few changes to dcm2mnc lately that might address your
issues. Have you tried the version from the latest minc-toolkit?

http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit

If that doesn't help, I'd be happy to help test with a GE sequence, if you
can provide one that exhibits the problem.

    -bert

On Wed, Aug 26, 2015 at 7:57 PM, Oury Monchi <Oury.Monchi at ucalgary.ca>
wrote:

> We have tried with v2 and had problems with 4d data Bold and DTI.
>
> Will try with v1 .
>
> Thank you,
> Oury.
>
> Sent from my HTC
>
> ----- Reply message -----
> From: "Jon Pipitone" <jon at pipitone.ca>
> To: "MINC users mailing list" <minc-users at bic.mni.mcgill.ca>
> Subject: [MINC-users] dcm2mnc GE 3T
> Date: Wed, Aug 26, 2015 5:54 PM
>
> Hi,
>
> We use dcm2mnc from minc-toolkit v1.0.01 on GE 3T scans all the time.
>
> Are you encountering problems?
>
> Jon.
>
> On Aug 26, 2015 5:14 PM, Oury Monchi <Oury.Monchi at ucalgary.ca> wrote:
> >
> > Dear all,
> >
> > I am trying to find out if there is a version of dcm2mnc that has been
> tried on dicom files from a GE 3T scanner.
> >
> > Best,
> > Oury.
> >
> > Oury Monchi, PhD
> >
> > Professor and Tourmaline Chair in Parkinson?s Disease
> >
> > Departments of Clinical Neurosciences and Radiology,
> > Leader of the Movement Disorders Research Neuroteam,
> >
> > Director of Clinical Research,
> >
> > Hotchkiss Brain Institute,
> >
> > Cumming School of Medicine, University of Calgary.
> > Tel: 403-2208048
> > E-mail:oury.monchi at ucalgary.ca
> > http://pcanlab.ca/
> >
> >
> > _______________________________________________
> > 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 Oury.Monchi at ucalgary.ca  Wed Aug 26 20:42:23 2015
From: Oury.Monchi at ucalgary.ca (Oury Monchi)
Date: Thu, 27 Aug 2015 00:42:23 +0000
Subject: [MINC-users] dcm2mnc GE 3T
In-Reply-To: <CAAd5DeRWTne8O7qEGyPqkVyXA8=SfqiNnSAbcx6S+7PJYL+r_w@mail.gmail.com>
References: <20150826235252.6C2F4318095@homiemail-a89.g.dreamhost.com>
	<5C8B702FE8D56248BE43D5CF0C69732D2BDB1327@ITCIMEXCH04.uc.ucalgary.ca>,
	<CAAd5DeRWTne8O7qEGyPqkVyXA8=SfqiNnSAbcx6S+7PJYL+r_w@mail.gmail.com>
Message-ID: <5C8B702FE8D56248BE43D5CF0C69732D2BDB1395@ITCIMEXCH04.uc.ucalgary.ca>

Thanks Robert,

Will test with that and come back to you if necessary.

Oury.

Sent from my HTC

----- Reply message -----
From: "Robert D. Vincent" <robert.d.vincent at mcgill.ca>
To: "MINC users mailing list" <minc-users at bic.mni.mcgill.ca>
Subject: [MINC-users] dcm2mnc GE 3T
Date: Wed, Aug 26, 2015 6:39 PM

Hi Oury,

We have made quite a few changes to dcm2mnc lately that might address your
issues. Have you tried the version from the latest minc-toolkit?

http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit

If that doesn't help, I'd be happy to help test with a GE sequence, if you
can provide one that exhibits the problem.

    -bert

On Wed, Aug 26, 2015 at 7:57 PM, Oury Monchi <Oury.Monchi at ucalgary.ca>
wrote:

> We have tried with v2 and had problems with 4d data Bold and DTI.
>
> Will try with v1 .
>
> Thank you,
> Oury.
>
> Sent from my HTC
>
> ----- Reply message -----
> From: "Jon Pipitone" <jon at pipitone.ca>
> To: "MINC users mailing list" <minc-users at bic.mni.mcgill.ca>
> Subject: [MINC-users] dcm2mnc GE 3T
> Date: Wed, Aug 26, 2015 5:54 PM
>
> Hi,
>
> We use dcm2mnc from minc-toolkit v1.0.01 on GE 3T scans all the time.
>
> Are you encountering problems?
>
> Jon.
>
> On Aug 26, 2015 5:14 PM, Oury Monchi <Oury.Monchi at ucalgary.ca> wrote:
> >
> > Dear all,
> >
> > I am trying to find out if there is a version of dcm2mnc that has been
> tried on dicom files from a GE 3T scanner.
> >
> > Best,
> > Oury.
> >
> > Oury Monchi, PhD
> >
> > Professor and Tourmaline Chair in Parkinson?s Disease
> >
> > Departments of Clinical Neurosciences and Radiology,
> > Leader of the Movement Disorders Research Neuroteam,
> >
> > Director of Clinical Research,
> >
> > Hotchkiss Brain Institute,
> >
> > Cumming School of Medicine, University of Calgary.
> > Tel: 403-2208048
> > E-mail:oury.monchi at ucalgary.ca
> > http://pcanlab.ca/
> >
> >
> > _______________________________________________
> > 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