From a.janke at gmail.com  Sun Jan  4 20:04:32 2015
From: a.janke at gmail.com (Andrew Janke)
Date: Mon, 5 Jan 2015 11:04:32 +1000
Subject: [MINC-users] mincresample -keep_real_range on float volume
In-Reply-To: <CABEEk16-c3mJuJ1PMsUPHun06JpD9ygjKiXBGMfXo1FCOa1bqA@mail.gmail.com>
References: <CABEEk16-c3mJuJ1PMsUPHun06JpD9ygjKiXBGMfXo1FCOa1bqA@mail.gmail.com>
Message-ID: <CAG0CB223pSiWBoMb_k_DAwu7aw2Psb+n3xisbtT=XZD18_0TJQ@mail.gmail.com>

Hi Alex,

I haven't tried this, but what does the output volume look like?

As you say, what you are attempting to do doesn't make much sense and
remember that mincstats isn't reporting the valid range but rather on
the values themselves. Thus I'm surprised at the +/- DBL_MAX values
being output, especially as the min is larger than the max!

I'm guessing the values being output are the default max and min
before running through the volume, so all the data is null?


a

On 31 December 2014 at 02:27, Alex Zijdenbos <zijdenbos at gmail.com> wrote:
> Hi all,
>
> It appears that running mincresample on a float volume while using
> -keep_real_range, fails. A simple example:
>
> $ mincreshape -float
> /usr/local/bic/share/mni-models/icbm_avg_152_t1_tal_lin.mnc float.mnc
> $ mincstats -quiet -min -max float.mnc
> 236.8016205
> 439776.2188
>
> $ mincresample -keep_real_range float.mnc float_res.mnc
> $ mincstats -quiet -min -max float_res.mnc
> 1.797693135e+308
> -1.797693135e+308
>
> Leaving aside why you'd want to use that option on a float volume (happened
> buried in a script in my case); what should the correct behaviour be?
> Ignore the -keep_real_range option for float volumes I'd imagine?
>
> Happy 2015 in advance!
>
> :-)
>
> -- A
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From bert at bic.mni.mcgill.ca  Mon Jan  5 10:53:49 2015
From: bert at bic.mni.mcgill.ca (Robert VINCENT)
Date: Mon, 5 Jan 2015 10:53:49 -0500 (EST)
Subject: [MINC-users] mincresample -keep_real_range on float volume
In-Reply-To: <CAG0CB223pSiWBoMb_k_DAwu7aw2Psb+n3xisbtT=XZD18_0TJQ@mail.gmail.com>
References: <CABEEk16-c3mJuJ1PMsUPHun06JpD9ygjKiXBGMfXo1FCOa1bqA@mail.gmail.com>
	<CAG0CB223pSiWBoMb_k_DAwu7aw2Psb+n3xisbtT=XZD18_0TJQ@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.1501051049240.29265@agrippa.bic.mni.mcgill.ca>

Hi,

I just reproduced this. The issue is that, at least in this example, the 
image:valid_range for float_res.mnc is being set to [0,1], while the true 
voxel values remain in the range [246.8016, 439776.2]. This must cause 
mincstats to ignore all of the values outside the valid_range, and 
therefore to print the min and max values as initialized.

I assume there is a simple bug in determining the valid_range for 
the output file. I'll see about fixing this soon.

Thanks for the report, Alex.

     -bert

On Mon, 5 Jan 2015, Andrew Janke wrote:

> Hi Alex,
>
> I haven't tried this, but what does the output volume look like?
>
> As you say, what you are attempting to do doesn't make much sense and
> remember that mincstats isn't reporting the valid range but rather on
> the values themselves. Thus I'm surprised at the +/- DBL_MAX values
> being output, especially as the min is larger than the max!
>
> I'm guessing the values being output are the default max and min
> before running through the volume, so all the data is null?
>
>
> a
>
> On 31 December 2014 at 02:27, Alex Zijdenbos <zijdenbos at gmail.com> wrote:
>> Hi all,
>>
>> It appears that running mincresample on a float volume while using
>> -keep_real_range, fails. A simple example:
>>
>> $ mincreshape -float
>> /usr/local/bic/share/mni-models/icbm_avg_152_t1_tal_lin.mnc float.mnc
>> $ mincstats -quiet -min -max float.mnc
>> 236.8016205
>> 439776.2188
>>
>> $ mincresample -keep_real_range float.mnc float_res.mnc
>> $ mincstats -quiet -min -max float_res.mnc
>> 1.797693135e+308
>> -1.797693135e+308
>>
>> Leaving aside why you'd want to use that option on a float volume (happened
>> buried in a script in my case); what should the correct behaviour be?
>> Ignore the -keep_real_range option for float volumes I'd imagine?
>>
>> Happy 2015 in advance!
>>
>> :-)
>>
>> -- 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 gdevenyi at gmail.com  Tue Jan  6 10:12:44 2015
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Tue, 6 Jan 2015 10:12:44 -0500
Subject: [MINC-users] CIVET-1.1.12 and sqrt(2) offset
Message-ID: <CAFQOoOpgV_22v_Uj5t+VstFQBKKD=jOBjDgkiXQknMh137nVgA@mail.gmail.com>

Hi all,

I was previously aware that CIVET-1.1.12 has a sqrt(2) mistake according to
the CIVET-2.0 changelog: "corrected fwhm for surface smoothing (was off by
sqrt(2) in 1.1.12)"

Is the "fwhw for surface smoothing" one of the command-line parameters that
could be adjusted to compensate? (my only guess is is "-area-fwhm <fwhm>")
If so, is it bigger or smaller by sqrt(2)?

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 claude at bic.mni.mcgill.ca  Tue Jan  6 10:39:34 2015
From: claude at bic.mni.mcgill.ca (Claude LEPAGE)
Date: Tue, 6 Jan 2015 10:39:34 -0500
Subject: [MINC-users] CIVET-1.1.12 and sqrt(2) offset
In-Reply-To: <CAFQOoOpgV_22v_Uj5t+VstFQBKKD=jOBjDgkiXQknMh137nVgA@mail.gmail.com>
Message-ID: <201501061539.t06FdYKt016617@agrippa.bic.mni.mcgill.ca>

Hi,

You have to multiply by sqrt(2) to obtain the correct fwhm in 
CIVET-1.1.12 for surface blurring.

-thickness tlink fwhm_desired*sqrt(2)
-area-fwhm fwhm_desired*sqrt(2)
-volume-fwhm fwhm_desired*sqrt(2)

For example, if you want fwhm=20mm, you have to specify
20*sqrt(2)=28.28. However, since fwhm is used in the 
filename for the thickness files, I suggest to round 
fwhm if you don't want filenames with a dot in them. 

If you used a value of 30mm before, then this corresponds
to an effective fwhm of 30/sqrt(2)=21.21mm. 

Sorry for the inconvenience.

Claude


>
> Hi all,
>
> I was previously aware that CIVET-1.1.12 has a sqrt(2) mistake according to
> the CIVET-2.0 changelog: "corrected fwhm for surface smoothing (was off by
> sqrt(2) in 1.1.12)"
>
> Is the "fwhw for surface smoothing" one of the command-line parameters that
> could be adjusted to compensate? (my only guess is is "-area-fwhm <fwhm>")
> If so, is it bigger or smaller by sqrt(2)?
>
> 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 gdevenyi at gmail.com  Tue Jan  6 10:46:36 2015
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Tue, 6 Jan 2015 10:46:36 -0500
Subject: [MINC-users] CIVET-1.1.12 and sqrt(2) offset
In-Reply-To: <201501061539.t06FdYKt016617@agrippa.bic.mni.mcgill.ca>
References: <CAFQOoOpgV_22v_Uj5t+VstFQBKKD=jOBjDgkiXQknMh137nVgA@mail.gmail.com>
	<201501061539.t06FdYKt016617@agrippa.bic.mni.mcgill.ca>
Message-ID: <CAFQOoOphpgcRMFC+q7=FmRYzxx45HjZSawGF_uR=9ueX0nTciA@mail.gmail.com>

Thanks so much!

Perhaps this info would make a helpful note on the CIVET-1.1.12
documentation page?

-- 
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 Tue, Jan 6, 2015 at 10:39 AM, Claude LEPAGE <claude at bic.mni.mcgill.ca>
wrote:

> Hi,
>
> You have to multiply by sqrt(2) to obtain the correct fwhm in
> CIVET-1.1.12 for surface blurring.
>
> -thickness tlink fwhm_desired*sqrt(2)
> -area-fwhm fwhm_desired*sqrt(2)
> -volume-fwhm fwhm_desired*sqrt(2)
>
> For example, if you want fwhm=20mm, you have to specify
> 20*sqrt(2)=28.28. However, since fwhm is used in the
> filename for the thickness files, I suggest to round
> fwhm if you don't want filenames with a dot in them.
>
> If you used a value of 30mm before, then this corresponds
> to an effective fwhm of 30/sqrt(2)=21.21mm.
>
> Sorry for the inconvenience.
>
> Claude
>
>
> >
> > Hi all,
> >
> > I was previously aware that CIVET-1.1.12 has a sqrt(2) mistake according
> to
> > the CIVET-2.0 changelog: "corrected fwhm for surface smoothing (was off
> by
> > sqrt(2) in 1.1.12)"
> >
> > Is the "fwhw for surface smoothing" one of the command-line parameters
> that
> > could be adjusted to compensate? (my only guess is is "-area-fwhm
> <fwhm>")
> > If so, is it bigger or smaller by sqrt(2)?
> >
> > 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 andrew at biospective.com  Tue Jan  6 11:27:21 2015
From: andrew at biospective.com (Andrew Wood)
Date: Tue, 6 Jan 2015 11:27:21 -0500
Subject: [MINC-users] Optimizing minc-toolkit builds
Message-ID: <CABApf9HRCdMwFfkTuTPU92au=SU3LhR8sjTPqb9vugzAG+AiEQ@mail.gmail.com>

Hi all,

I'm building minc-toolkit (release-1.9.06) from github and wondering about
the best way to get production-appropriate options passed to gcc/g++.

The simplest build procedure ...

$ mkdir build && cd build
$ cmake ..
$ make

... seems to leave most modules unoptimized.

Should I be specifying these things manually with CMAKE_C{,XX}_FLAGS at the
cmake call, or is there a "production" or "release" switch that can be used?

Thanks,
Andrew

From vladimir.fonov at gmail.com  Tue Jan  6 11:40:59 2015
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Tue, 6 Jan 2015 11:40:59 -0500
Subject: [MINC-users] Optimizing minc-toolkit builds
In-Reply-To: <CABApf9HRCdMwFfkTuTPU92au=SU3LhR8sjTPqb9vugzAG+AiEQ@mail.gmail.com>
References: <CABApf9HRCdMwFfkTuTPU92au=SU3LhR8sjTPqb9vugzAG+AiEQ@mail.gmail.com>
Message-ID: <CAMCwi7PXXrs_tX_5VDtRYrnq4pha+zSeo3bJid3oaxDhrf2Q-w@mail.gmail.com>

you should set CMAKE_BUILD_TYPE to Release

On Tue, Jan 6, 2015 at 11:27 AM, Andrew Wood <andrew at biospective.com> wrote:

> Hi all,
>
> I'm building minc-toolkit (release-1.9.06) from github and wondering about
> the best way to get production-appropriate options passed to gcc/g++.
>
> The simplest build procedure ...
>
> $ mkdir build && cd build
> $ cmake ..
> $ make
>
> ... seems to leave most modules unoptimized.
>
> Should I be specifying these things manually with CMAKE_C{,XX}_FLAGS at the
> cmake call, or is there a "production" or "release" switch that can be
> used?
>
> Thanks,
> Andrew
> _______________________________________________
> 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

From andrew at biospective.com  Tue Jan  6 11:46:25 2015
From: andrew at biospective.com (Andrew Wood)
Date: Tue, 6 Jan 2015 11:46:25 -0500
Subject: [MINC-users] Optimizing minc-toolkit builds
In-Reply-To: <CAMCwi7PXXrs_tX_5VDtRYrnq4pha+zSeo3bJid3oaxDhrf2Q-w@mail.gmail.com>
References: <CABApf9HRCdMwFfkTuTPU92au=SU3LhR8sjTPqb9vugzAG+AiEQ@mail.gmail.com>
	<CAMCwi7PXXrs_tX_5VDtRYrnq4pha+zSeo3bJid3oaxDhrf2Q-w@mail.gmail.com>
Message-ID: <CABApf9EzboNNip__SR_5+_+anGjyGjYC=omvMaPMoyJeCadDAQ@mail.gmail.com>

Perfect!

Thanks,
Andrew

On Tue, Jan 6, 2015 at 11:40 AM, Vladimir S. FONOV <vladimir.fonov at gmail.com
> wrote:

> you should set CMAKE_BUILD_TYPE to Release
>
> On Tue, Jan 6, 2015 at 11:27 AM, Andrew Wood <andrew at biospective.com>
> wrote:
>
> > Hi all,
> >
> > I'm building minc-toolkit (release-1.9.06) from github and wondering
> about
> > the best way to get production-appropriate options passed to gcc/g++.
> >
> > The simplest build procedure ...
> >
> > $ mkdir build && cd build
> > $ cmake ..
> > $ make
> >
> > ... seems to leave most modules unoptimized.
> >
> > Should I be specifying these things manually with CMAKE_C{,XX}_FLAGS at
> the
> > cmake call, or is there a "production" or "release" switch that can be
> > used?
> >
> > Thanks,
> > Andrew
> > _______________________________________________
> > 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
>

From gdevenyi at gmail.com  Wed Jan  7 14:15:39 2015
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Wed, 7 Jan 2015 14:15:39 -0500
Subject: [MINC-users] Providing masks in CIVET?
Message-ID: <CAFQOoOrG-fmsSGv_Pq7M35BHV-UmOaHJrW7UM==iRvVrXCEkyw@mail.gmail.com>

Hi all,

I have a question regarding the specification of masks for CIVET. I see
that CIVET uses mincbet to produce brain masks during its processing and
that it is possible to provide pre-generated masks (from something like
BeAST).

Where do these masks come into play during processing and if they're not
perfect is there a possibility of screwing up the processing? I would
expect that BeAST generated masks will be superior to mincbet masks in most
cases.

Thanks for your help!

-- 
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 claude at bic.mni.mcgill.ca  Wed Jan  7 18:03:19 2015
From: claude at bic.mni.mcgill.ca (Claude LEPAGE)
Date: Wed, 7 Jan 2015 18:03:19 -0500
Subject: [MINC-users] Providing masks in CIVET?
In-Reply-To: <CAFQOoOrG-fmsSGv_Pq7M35BHV-UmOaHJrW7UM==iRvVrXCEkyw@mail.gmail.com>
Message-ID: <201501072303.t07N3J5A028285@agrippa.bic.mni.mcgill.ca>

Hi Gabriel,

mincbet is an improved version of FSL bet, based on minc volumes.
The masks from mincbet are generally excellent, except in some 
extreme cases (infants, pathologies with huge ventricles in old
subjects).

The mask in CIVET-1.1.12 and CIVET-2.0.0 is used as a white matter
mask only. It is not used as a gray matter mask. The pial boundary
is determined by expansion of the white surface up to CSF. It is
very rare that the mask will truncate white matter. Beware that
the mask has evolved greatly since CIVET-1.1.11 when a comparison
between BeAST and an older version of mincbet was done..

Claude

>
> Hi all,
>
> I have a question regarding the specification of masks for CIVET. I see
> that CIVET uses mincbet to produce brain masks during its processing and
> that it is possible to provide pre-generated masks (from something like
> BeAST).
>
> Where do these masks come into play during processing and if they're not
> perfect is there a possibility of screwing up the processing? I would
> expect that BeAST generated masks will be superior to mincbet masks in most
> cases.
>
> Thanks for your help!
>
> -- 
> 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 pierre.bellec at criugm.qc.ca  Thu Jan  8 00:33:24 2015
From: pierre.bellec at criugm.qc.ca (Pierre Bellec)
Date: Thu, 8 Jan 2015 00:33:24 -0500
Subject: [MINC-users] functional brain parcellations
Message-ID: <CADPHwxD27BcTbueo6xbpWxony_BTtSdYPwQBvHxxhrtNMbaprA@mail.gmail.com>

Dear minc users,

As brain parcellations can be handy for a number of purposes, I wanted to
let you I just released a set of group brain parcellations, with different
number of parcels, ranging from 7 to 400+. The parcels have been generated
by clustering resting-state fMRI time series, so low scales match pretty
well the standard resting-state networks, while higher scales are
subnetworks, down to regions. The parcellations can be found here:

http://figshare.com/articles/Group_multiscale_functional_template_generated_with_BASC_on_the_Cambridge_sample/1285615

The parcellations are available in nifti and mnc1. They also live in the
MNI 2009 space, either symmetric or asymmetric. Finally, being functional,
they are at 3 mm resolution.

Best regards,

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

From a.janke at gmail.com  Wed Jan 14 23:22:50 2015
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 15 Jan 2015 14:22:50 +1000
Subject: [MINC-users] img2mnc
Message-ID: <CAG0CB22WaV0gceD527U-e0=wZmP6pPqQVLP1TF-UjeY9__=C2w@mail.gmail.com>

Hi all,

Those who deal with histology data will likely be interested in this:

https://github.com/BIC-MNI/minc-widgets/blob/master/img2mnc/img2mnc

It's part of minc-toolkit so you should see the updates when Vladimir
releases a new version.NAME
       img2mnc - convert an image (PNG, JPG, etc) to MINC

a


$ img2mnc -man
IMG2MNC(1)            User Contributed Perl Documentation           IMG2MNC(1)

NAME
       img2mnc - convert an image (PNG, JPG, etc) to MINC

SYNOPSIS
       img2mnc [options] <infile1.{png|jpg|tif|gif}> [<infile2.png>]
<outfile.mnc>

       img2mnc takes an input image (any format readable by
imagemagick) and converts it to MINC

DESCRIPTION
       img2mnc arose out of the need from converting multiple
histology formats to MINC. This is fine for the major formats but you
often have
       to deal with data in common tif, jpg or PNG form.

       img2mnc will attempt to deduce the step sizes from the input
files based upon their resolution but this is not always correct. If
this
       turns out to be incorrect you will need to correct this later
using mincedit or minc_modify_header.

       Typical usage example for a single input file:

           $ img2mnc in.png out.mnc

       Typical usage for an input set of RGB files with a bitdepth of
16 (unsigned short)

           $ img2mnc -rgb input???.png out.mnc

OPTIONS
       -v, --verbose
           Be noisy when doing things (most importantly this will echo
the resulting script to the terminal)

       --version
           Print version number and exit

       -c, --clobber
           Overwrite existing files

       -h, --help
           Dump some quick help output

       --man
           Dump a man page

       -f, --fake
           Do a dry run. This is usually only useful if combined with
--verbose so that you can see what is going on.

       -t, --tmpdir
           Define a tmpdir in which to place temporary files while processing

       --keeptmp
           Don't remove the tmpdir when complete (usefull for debugging)

       --filelist
           Specify a file that contains a list of input filenames
instead of using those from the command line

       --slice_step
           Specify a slice spacing, this is typically the Z dimension

       --slice_start
           Specify a slice start, this is typically the Z dimension

       --rgb
           Convert the data as RGB resulting in a 4D file

       --depth
           Convert the data at the desired bitdepth. Currently only 8
(byte) and 16 (unsigned short) are supported.

AUTHOR
       Problems or Comments to: Andrew Janke - a.janke at gmail.com

From pgravel at bic.mni.mcgill.ca  Tue Jan 20 15:24:36 2015
From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL)
Date: Tue, 20 Jan 2015 15:24:36 -0500 (EST)
Subject: [MINC-users] Outputting overlay of co-registered MINC files
	directly to a file
In-Reply-To: <CAG0CB22WaV0gceD527U-e0=wZmP6pPqQVLP1TF-UjeY9__=C2w@mail.gmail.com>
References: <CAG0CB22WaV0gceD527U-e0=wZmP6pPqQVLP1TF-UjeY9__=C2w@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.1501201513190.8959@agrippa.bic.mni.mcgill.ca>

Dear All,

I am currently doing a bunch of co-registrations (PET to MR , and PET to 
STX space) and I was wondering if there was an alternative to opening 
register everytime to visually inspect the co-registration between the two 
volumes, i.e. is it possible (does a tool exist?) to output the overlayed 
volumes (for a few sllices only), as shown in the right-hand column of 
register, directly to an image file (e.g. .png), without having to open 
register? One could then scroll through the series of the overlaid slices 
for a quality check, or put these images (while running a script) in a 
quality assessment report.
I vaguely remember old tools/scripts (either do_mritopet or do_mritotal) 
doing something similar.
Any ideas?
Best Regards,
Paul

From claude at bic.mni.mcgill.ca  Tue Jan 20 15:31:32 2015
From: claude at bic.mni.mcgill.ca (Claude LEPAGE)
Date: Tue, 20 Jan 2015 15:31:32 -0500
Subject: [MINC-users] Outputting overlay of co-registered MINC files
	directly to a file
In-Reply-To: <Pine.LNX.4.64.1501201513190.8959@agrippa.bic.mni.mcgill.ca>
Message-ID: <201501202031.t0KKVWZt011465@agrippa.bic.mni.mcgill.ca>

Hi Paul,

Try something like this, in Perlish way:

  `mincpik -clobber -slice 100 -axial -width 300 -lookup -spectral $input /tmp/axial.jpg`;
  `mincpik -clobber -slice 100 -coronal -width 300 -lookup -spectral $input /tmp/coronal.jpg`;
  `mincpik -clobber -slice 100 -sagittal -width 300 -lookup -spectral $input /tmp/sagittal.jpg`;
  `montage -tile 3x1 -background black -geometry 300x300+1+1 /tmp/axial.jpg /tmp/coronal.jpg /tmp/sagittal.jpg image_t1.jpg`;

$input is you minc file in stx space. You can play with the
colour scheme if you don't like spectral. 

I do the above in a script when I convert from DICOM/nii to minc
in order to check the sanity of the minc files.

Claude

From vladimir.fonov at gmail.com  Tue Jan 20 15:36:47 2015
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Tue, 20 Jan 2015 15:36:47 -0500
Subject: [MINC-users] Outputting overlay of co-registered MINC files
 directly to a file
In-Reply-To: <Pine.LNX.4.64.1501201513190.8959@agrippa.bic.mni.mcgill.ca>
References: <CAG0CB22WaV0gceD527U-e0=wZmP6pPqQVLP1TF-UjeY9__=C2w@mail.gmail.com>
	<Pine.LNX.4.64.1501201513190.8959@agrippa.bic.mni.mcgill.ca>
Message-ID: <CAMCwi7PG_iUx7_-FPSg8RipJrSD=NYnoFET7sdibGD9gefBiHg@mail.gmail.com>

Hello,

you can use minc_qc.pl script for that , something like that:

minc_qc.pl  t1w.mnc t1w_qc.jpg
       --mask  overlay.mnc --title "subject_1 --image-range 5 100
--mask-range 5 20 --big


will produce  a series of pictures with overlay of t1w scan (in gray) and
overlay.mnc (in red)





On Tue, Jan 20, 2015 at 3:24 PM, Paul GRAVEL <pgravel at bic.mni.mcgill.ca>
wrote:

> Dear All,
>
> I am currently doing a bunch of co-registrations (PET to MR , and PET to
> STX space) and I was wondering if there was an alternative to opening
> register everytime to visually inspect the co-registration between the two
> volumes, i.e. is it possible (does a tool exist?) to output the overlayed
> volumes (for a few sllices only), as shown in the right-hand column of
> register, directly to an image file (e.g. .png), without having to open
> register? One could then scroll through the series of the overlaid slices
> for a quality check, or put these images (while running a script) in a
> quality assessment report.
> I vaguely remember old tools/scripts (either do_mritopet or do_mritotal)
> doing something similar.
> Any ideas?
> Best Regards,
> Paul
> _______________________________________________
> 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

From pgravel at bic.mni.mcgill.ca  Tue Jan 20 17:17:10 2015
From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL)
Date: Tue, 20 Jan 2015 17:17:10 -0500 (EST)
Subject: [MINC-users] Outputting overlay of co-registered MINC files
 directly to a file
In-Reply-To: <CAMCwi7PG_iUx7_-FPSg8RipJrSD=NYnoFET7sdibGD9gefBiHg@mail.gmail.com>
References: <CAG0CB22WaV0gceD527U-e0=wZmP6pPqQVLP1TF-UjeY9__=C2w@mail.gmail.com>
	<Pine.LNX.4.64.1501201513190.8959@agrippa.bic.mni.mcgill.ca>
	<CAMCwi7PG_iUx7_-FPSg8RipJrSD=NYnoFET7sdibGD9gefBiHg@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.1501201706100.27209@agrippa.bic.mni.mcgill.ca>

Once again, Many Thanks Claude and Vladimir for your replies!

Just what I was looking for!
Although, I ended up using minc_qc.pl ;-)!

Best,

Paul

On Tue, 20 Jan 2015, Vladimir S. FONOV wrote:

> Hello,
>
> you can use minc_qc.pl script for that , something like that:
>
> minc_qc.pl  t1w.mnc t1w_qc.jpg
>       --mask  overlay.mnc --title "subject_1 --image-range 5 100
> --mask-range 5 20 --big
>
>
> will produce  a series of pictures with overlay of t1w scan (in gray) and
> overlay.mnc (in red)
>
>
>
>
>
> On Tue, Jan 20, 2015 at 3:24 PM, Paul GRAVEL <pgravel at bic.mni.mcgill.ca>
> wrote:
>
>> Dear All,
>>
>> I am currently doing a bunch of co-registrations (PET to MR , and PET to
>> STX space) and I was wondering if there was an alternative to opening
>> register everytime to visually inspect the co-registration between the two
>> volumes, i.e. is it possible (does a tool exist?) to output the overlayed
>> volumes (for a few sllices only), as shown in the right-hand column of
>> register, directly to an image file (e.g. .png), without having to open
>> register? One could then scroll through the series of the overlaid slices
>> for a quality check, or put these images (while running a script) in a
>> quality assessment report.
>> I vaguely remember old tools/scripts (either do_mritopet or do_mritotal)
>> doing something similar.
>> Any ideas?
>> Best Regards,
>> Paul
>> _______________________________________________
>> 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
>

From a.janke at gmail.com  Tue Jan 20 18:44:00 2015
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 21 Jan 2015 09:44:00 +1000
Subject: [MINC-users] Outputting overlay of co-registered MINC files
 directly to a file
In-Reply-To: <201501202031.t0KKVWZt011465@agrippa.bic.mni.mcgill.ca>
References: <Pine.LNX.4.64.1501201513190.8959@agrippa.bic.mni.mcgill.ca>
	<201501202031.t0KKVWZt011465@agrippa.bic.mni.mcgill.ca>
Message-ID: <CAG0CB22kBZxmtWPt=QCTP3-wXVAfNnqF-gMbGeoYXXyhotyGzg@mail.gmail.com>

Claude and Vladimir's suggestions will certainly do what you are
requesting, but in case others are watching on, here is a somewhat
easier way to achieve what Claude posted albeit with slightly less
control on the chosen slice(s).

   mincpik -triplanar -tilesize 300 -horizontal -title "bob the cat"
input.mnc out.jpg

If like me, you'd like a slice offset from the centre by 10% of the
volume size in the sagittal direction then do this:

   mincpik -triplanar -tilesize 300 -horizontal -title "bob the cat"
-sagittal_offset_perc 10 input.mnc out.jpg


a

On 21 January 2015 at 06:31, Claude LEPAGE <claude at bic.mni.mcgill.ca> wrote:
> Hi Paul,
>
> Try something like this, in Perlish way:
>
>   `mincpik -clobber -slice 100 -axial -width 300 -lookup -spectral $input /tmp/axial.jpg`;
>   `mincpik -clobber -slice 100 -coronal -width 300 -lookup -spectral $input /tmp/coronal.jpg`;
>   `mincpik -clobber -slice 100 -sagittal -width 300 -lookup -spectral $input /tmp/sagittal.jpg`;
>   `montage -tile 3x1 -background black -geometry 300x300+1+1 /tmp/axial.jpg /tmp/coronal.jpg /tmp/sagittal.jpg image_t1.jpg`;
>
> $input is you minc file in stx space. You can play with the
> colour scheme if you don't like spectral.
>
> I do the above in a script when I convert from DICOM/nii to minc
> in order to check the sanity of the minc files.
>
> Claude
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From zijdenbos at gmail.com  Tue Jan 20 20:26:26 2015
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Tue, 20 Jan 2015 20:26:26 -0500
Subject: [MINC-users] Outputting overlay of co-registered MINC files
 directly to a file
In-Reply-To: <CAG0CB22kBZxmtWPt=QCTP3-wXVAfNnqF-gMbGeoYXXyhotyGzg@mail.gmail.com>
References: <Pine.LNX.4.64.1501201513190.8959@agrippa.bic.mni.mcgill.ca>
	<201501202031.t0KKVWZt011465@agrippa.bic.mni.mcgill.ca>
	<CAG0CB22kBZxmtWPt=QCTP3-wXVAfNnqF-gMbGeoYXXyhotyGzg@mail.gmail.com>
Message-ID: <CABEEk167VTaivOLa9AY5xYLAEcpYRm9w+09jFPKLfy=x53D0sw@mail.gmail.com>

Or you can use create_verify_image (bundled with ILT), and pretty simply
create images like these:

PET to T1 <https://dl.dropboxusercontent.com/u/5709165/MINC/PET2T1_stx.png>
PET stx <https://dl.dropboxusercontent.com/u/5709165/MINC/PET_stx.png>

-- A


On Tue, Jan 20, 2015 at 6:44 PM, Andrew Janke <a.janke at gmail.com> wrote:

> Claude and Vladimir's suggestions will certainly do what you are
> requesting, but in case others are watching on, here is a somewhat
> easier way to achieve what Claude posted albeit with slightly less
> control on the chosen slice(s).
>
>    mincpik -triplanar -tilesize 300 -horizontal -title "bob the cat"
> input.mnc out.jpg
>
> If like me, you'd like a slice offset from the centre by 10% of the
> volume size in the sagittal direction then do this:
>
>    mincpik -triplanar -tilesize 300 -horizontal -title "bob the cat"
> -sagittal_offset_perc 10 input.mnc out.jpg
>
>
> a
>
> On 21 January 2015 at 06:31, Claude LEPAGE <claude at bic.mni.mcgill.ca>
> wrote:
> > Hi Paul,
> >
> > Try something like this, in Perlish way:
> >
> >   `mincpik -clobber -slice 100 -axial -width 300 -lookup -spectral
> $input /tmp/axial.jpg`;
> >   `mincpik -clobber -slice 100 -coronal -width 300 -lookup -spectral
> $input /tmp/coronal.jpg`;
> >   `mincpik -clobber -slice 100 -sagittal -width 300 -lookup -spectral
> $input /tmp/sagittal.jpg`;
> >   `montage -tile 3x1 -background black -geometry 300x300+1+1
> /tmp/axial.jpg /tmp/coronal.jpg /tmp/sagittal.jpg image_t1.jpg`;
> >
> > $input is you minc file in stx space. You can play with the
> > colour scheme if you don't like spectral.
> >
> > I do the above in a script when I convert from DICOM/nii to minc
> > in order to check the sanity of the minc files.
> >
> > 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
>
>

From gdevenyi at gmail.com  Thu Jan 22 17:26:11 2015
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Thu, 22 Jan 2015 17:26:11 -0500
Subject: [MINC-users] mincANTS initial affine parameter
Message-ID: <CAFQOoOrfBFrcaVxCK5V8p_DcVLvo_oEFYJEoeaQJr2TYgVd2_Q@mail.gmail.com>

Hi all,

A question about the mincANTS implementation,

When mincANTS is invoked with -a initial_transformation.xfm, will the
resulting output XFMs include the transformations in
initial_transformation.xfm or are they applied on top of that initial
transformation?

Thanks for your help.
?
-- 
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 pgravel at bic.mni.mcgill.ca  Fri Jan 23 14:24:50 2015
From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL)
Date: Fri, 23 Jan 2015 14:24:50 -0500 (EST)
Subject: [MINC-users] Outputting overlay of co-registered MINC files
 directly to a file
In-Reply-To: <CABEEk167VTaivOLa9AY5xYLAEcpYRm9w+09jFPKLfy=x53D0sw@mail.gmail.com>
References: <Pine.LNX.4.64.1501201513190.8959@agrippa.bic.mni.mcgill.ca>
	<201501202031.t0KKVWZt011465@agrippa.bic.mni.mcgill.ca>
	<CAG0CB22kBZxmtWPt=QCTP3-wXVAfNnqF-gMbGeoYXXyhotyGzg@mail.gmail.com>
	<CABEEk167VTaivOLa9AY5xYLAEcpYRm9w+09jFPKLfy=x53D0sw@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.1501231422550.2125@agrippa.bic.mni.mcgill.ca>

Thanks also Alex and Andrew!
Alex, very nice images!
I will look into using this tool more closely.
Best,
Paul


On Tue, 20 Jan 2015, Alex Zijdenbos wrote:

> Or you can use create_verify_image (bundled with ILT), and pretty simply
> create images like these:
>
> PET to T1 <https://dl.dropboxusercontent.com/u/5709165/MINC/PET2T1_stx.png>
> PET stx <https://dl.dropboxusercontent.com/u/5709165/MINC/PET_stx.png>
>
> -- A
>
>
> On Tue, Jan 20, 2015 at 6:44 PM, Andrew Janke <a.janke at gmail.com> wrote:
>
>> Claude and Vladimir's suggestions will certainly do what you are
>> requesting, but in case others are watching on, here is a somewhat
>> easier way to achieve what Claude posted albeit with slightly less
>> control on the chosen slice(s).
>>
>>    mincpik -triplanar -tilesize 300 -horizontal -title "bob the cat"
>> input.mnc out.jpg
>>
>> If like me, you'd like a slice offset from the centre by 10% of the
>> volume size in the sagittal direction then do this:
>>
>>    mincpik -triplanar -tilesize 300 -horizontal -title "bob the cat"
>> -sagittal_offset_perc 10 input.mnc out.jpg
>>
>>
>> a
>>
>> On 21 January 2015 at 06:31, Claude LEPAGE <claude at bic.mni.mcgill.ca>
>> wrote:
>>> Hi Paul,
>>>
>>> Try something like this, in Perlish way:
>>>
>>>   `mincpik -clobber -slice 100 -axial -width 300 -lookup -spectral
>> $input /tmp/axial.jpg`;
>>>   `mincpik -clobber -slice 100 -coronal -width 300 -lookup -spectral
>> $input /tmp/coronal.jpg`;
>>>   `mincpik -clobber -slice 100 -sagittal -width 300 -lookup -spectral
>> $input /tmp/sagittal.jpg`;
>>>   `montage -tile 3x1 -background black -geometry 300x300+1+1
>> /tmp/axial.jpg /tmp/coronal.jpg /tmp/sagittal.jpg image_t1.jpg`;
>>>
>>> $input is you minc file in stx space. You can play with the
>>> colour scheme if you don't like spectral.
>>>
>>> I do the above in a script when I convert from DICOM/nii to minc
>>> in order to check the sanity of the minc files.
>>>
>>> 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
>>
>>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From andrew at biospective.com  Fri Jan 23 14:46:12 2015
From: andrew at biospective.com (Andrew Wood)
Date: Fri, 23 Jan 2015 14:46:12 -0500
Subject: [MINC-users] Outputting overlay of co-registered MINC files
 directly to a file
In-Reply-To: <Pine.LNX.4.64.1501231422550.2125@agrippa.bic.mni.mcgill.ca>
References: <Pine.LNX.4.64.1501201513190.8959@agrippa.bic.mni.mcgill.ca>
	<201501202031.t0KKVWZt011465@agrippa.bic.mni.mcgill.ca>
	<CAG0CB22kBZxmtWPt=QCTP3-wXVAfNnqF-gMbGeoYXXyhotyGzg@mail.gmail.com>
	<CABEEk167VTaivOLa9AY5xYLAEcpYRm9w+09jFPKLfy=x53D0sw@mail.gmail.com>
	<Pine.LNX.4.64.1501231422550.2125@agrippa.bic.mni.mcgill.ca>
Message-ID: <CABApf9Hy4X-YCgY9MuC-Pg9cExGnYsEURZrEeQEBjgU-ELFZKQ@mail.gmail.com>

Hi all,

Alex's images are really easy to make with the create_verify_image script
that we're running here at Biospective. We've added quite a number of
convenience functions (e.g. on-the-fly marching_cubes for surface overlays,
thresholding options for volume overlays, etc).

His PET to T1 image would be made with a call like this:
$ create_verify_image PET2T1_stx.png  \
-autocols 4 -width 2400 \
-row t1_stx.mnc color:gray surface_overylay:csf_stx.mnc:blue \
-row PET_stx.mnc color:gray surface_overylay:csf_stx.mnc:blue

Does anyone know where the ILT source code lives, and who is maintaining
it? It'd be great if we could feed these improvements back to the community.

Best,
Andrew

On Fri, Jan 23, 2015 at 2:24 PM, Paul GRAVEL <pgravel at bic.mni.mcgill.ca>
wrote:

> Thanks also Alex and Andrew!
> Alex, very nice images!
> I will look into using this tool more closely.
> Best,
> Paul
>
>
>
> On Tue, 20 Jan 2015, Alex Zijdenbos wrote:
>
>  Or you can use create_verify_image (bundled with ILT), and pretty simply
>> create images like these:
>>
>> PET to T1 <https://dl.dropboxusercontent.com/u/
>> 5709165/MINC/PET2T1_stx.png>
>> PET stx <https://dl.dropboxusercontent.com/u/5709165/MINC/PET_stx.png>
>>
>> -- A
>>
>>
>> On Tue, Jan 20, 2015 at 6:44 PM, Andrew Janke <a.janke at gmail.com> wrote:
>>
>>  Claude and Vladimir's suggestions will certainly do what you are
>>> requesting, but in case others are watching on, here is a somewhat
>>> easier way to achieve what Claude posted albeit with slightly less
>>> control on the chosen slice(s).
>>>
>>>    mincpik -triplanar -tilesize 300 -horizontal -title "bob the cat"
>>> input.mnc out.jpg
>>>
>>> If like me, you'd like a slice offset from the centre by 10% of the
>>> volume size in the sagittal direction then do this:
>>>
>>>    mincpik -triplanar -tilesize 300 -horizontal -title "bob the cat"
>>> -sagittal_offset_perc 10 input.mnc out.jpg
>>>
>>>
>>> a
>>>
>>> On 21 January 2015 at 06:31, Claude LEPAGE <claude at bic.mni.mcgill.ca>
>>> wrote:
>>>
>>>> Hi Paul,
>>>>
>>>> Try something like this, in Perlish way:
>>>>
>>>>   `mincpik -clobber -slice 100 -axial -width 300 -lookup -spectral
>>>>
>>> $input /tmp/axial.jpg`;
>>>
>>>>   `mincpik -clobber -slice 100 -coronal -width 300 -lookup -spectral
>>>>
>>> $input /tmp/coronal.jpg`;
>>>
>>>>   `mincpik -clobber -slice 100 -sagittal -width 300 -lookup -spectral
>>>>
>>> $input /tmp/sagittal.jpg`;
>>>
>>>>   `montage -tile 3x1 -background black -geometry 300x300+1+1
>>>>
>>> /tmp/axial.jpg /tmp/coronal.jpg /tmp/sagittal.jpg image_t1.jpg`;
>>>
>>>>
>>>> $input is you minc file in stx space. You can play with the
>>>> colour scheme if you don't like spectral.
>>>>
>>>> I do the above in a script when I convert from DICOM/nii to minc
>>>> in order to check the sanity of the minc files.
>>>>
>>>> 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
>>>
>>>
>>>  _______________________________________________
>> 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  Fri Jan 23 14:49:44 2015
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Fri, 23 Jan 2015 14:49:44 -0500
Subject: [MINC-users] Outputting overlay of co-registered MINC files
 directly to a file
In-Reply-To: <CABApf9Hy4X-YCgY9MuC-Pg9cExGnYsEURZrEeQEBjgU-ELFZKQ@mail.gmail.com>
References: <Pine.LNX.4.64.1501201513190.8959@agrippa.bic.mni.mcgill.ca>
	<201501202031.t0KKVWZt011465@agrippa.bic.mni.mcgill.ca>
	<CAG0CB22kBZxmtWPt=QCTP3-wXVAfNnqF-gMbGeoYXXyhotyGzg@mail.gmail.com>
	<CABEEk167VTaivOLa9AY5xYLAEcpYRm9w+09jFPKLfy=x53D0sw@mail.gmail.com>
	<Pine.LNX.4.64.1501231422550.2125@agrippa.bic.mni.mcgill.ca>
	<CABApf9Hy4X-YCgY9MuC-Pg9cExGnYsEURZrEeQEBjgU-ELFZKQ@mail.gmail.com>
Message-ID: <CAMCwi7Mn5M1vbH3r64cZnQpVVi553dSpRKhYAcPhL64xhuicqw@mail.gmail.com>

Isn't it all part of CIVET?  Then Claude will be the one maintaining it.


On Fri, Jan 23, 2015 at 2:46 PM, Andrew Wood <andrew at biospective.com> wrote:

> Hi all,
>
> Alex's images are really easy to make with the create_verify_image script
> that we're running here at Biospective. We've added quite a number of
> convenience functions (e.g. on-the-fly marching_cubes for surface overlays,
> thresholding options for volume overlays, etc).
>
> His PET to T1 image would be made with a call like this:
> $ create_verify_image PET2T1_stx.png  \
> -autocols 4 -width 2400 \
> -row t1_stx.mnc color:gray surface_overylay:csf_stx.mnc:blue \
> -row PET_stx.mnc color:gray surface_overylay:csf_stx.mnc:blue
>
> Does anyone know where the ILT source code lives, and who is maintaining
> it? It'd be great if we could feed these improvements back to the
> community.
>
> Best,
> Andrew
>
> On Fri, Jan 23, 2015 at 2:24 PM, Paul GRAVEL <pgravel at bic.mni.mcgill.ca>
> wrote:
>
> > Thanks also Alex and Andrew!
> > Alex, very nice images!
> > I will look into using this tool more closely.
> > Best,
> > Paul
> >
> >
> >
> > On Tue, 20 Jan 2015, Alex Zijdenbos wrote:
> >
> >  Or you can use create_verify_image (bundled with ILT), and pretty simply
> >> create images like these:
> >>
> >> PET to T1 <https://dl.dropboxusercontent.com/u/
> >> 5709165/MINC/PET2T1_stx.png>
> >> PET stx <https://dl.dropboxusercontent.com/u/5709165/MINC/PET_stx.png>
> >>
> >> -- A
> >>
> >>
> >> On Tue, Jan 20, 2015 at 6:44 PM, Andrew Janke <a.janke at gmail.com>
> wrote:
> >>
> >>  Claude and Vladimir's suggestions will certainly do what you are
> >>> requesting, but in case others are watching on, here is a somewhat
> >>> easier way to achieve what Claude posted albeit with slightly less
> >>> control on the chosen slice(s).
> >>>
> >>>    mincpik -triplanar -tilesize 300 -horizontal -title "bob the cat"
> >>> input.mnc out.jpg
> >>>
> >>> If like me, you'd like a slice offset from the centre by 10% of the
> >>> volume size in the sagittal direction then do this:
> >>>
> >>>    mincpik -triplanar -tilesize 300 -horizontal -title "bob the cat"
> >>> -sagittal_offset_perc 10 input.mnc out.jpg
> >>>
> >>>
> >>> a
> >>>
> >>> On 21 January 2015 at 06:31, Claude LEPAGE <claude at bic.mni.mcgill.ca>
> >>> wrote:
> >>>
> >>>> Hi Paul,
> >>>>
> >>>> Try something like this, in Perlish way:
> >>>>
> >>>>   `mincpik -clobber -slice 100 -axial -width 300 -lookup -spectral
> >>>>
> >>> $input /tmp/axial.jpg`;
> >>>
> >>>>   `mincpik -clobber -slice 100 -coronal -width 300 -lookup -spectral
> >>>>
> >>> $input /tmp/coronal.jpg`;
> >>>
> >>>>   `mincpik -clobber -slice 100 -sagittal -width 300 -lookup -spectral
> >>>>
> >>> $input /tmp/sagittal.jpg`;
> >>>
> >>>>   `montage -tile 3x1 -background black -geometry 300x300+1+1
> >>>>
> >>> /tmp/axial.jpg /tmp/coronal.jpg /tmp/sagittal.jpg image_t1.jpg`;
> >>>
> >>>>
> >>>> $input is you minc file in stx space. You can play with the
> >>>> colour scheme if you don't like spectral.
> >>>>
> >>>> I do the above in a script when I convert from DICOM/nii to minc
> >>>> in order to check the sanity of the minc files.
> >>>>
> >>>> 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
> >>>
> >>>
> >>>  _______________________________________________
> >> 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
>



-- 
Best regards,

 Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com

From zijdenbos at gmail.com  Fri Jan 23 14:53:07 2015
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Fri, 23 Jan 2015 14:53:07 -0500
Subject: [MINC-users] Outputting overlay of co-registered MINC files
 directly to a file
In-Reply-To: <CAMCwi7Mn5M1vbH3r64cZnQpVVi553dSpRKhYAcPhL64xhuicqw@mail.gmail.com>
References: <Pine.LNX.4.64.1501201513190.8959@agrippa.bic.mni.mcgill.ca>
	<201501202031.t0KKVWZt011465@agrippa.bic.mni.mcgill.ca>
	<CAG0CB22kBZxmtWPt=QCTP3-wXVAfNnqF-gMbGeoYXXyhotyGzg@mail.gmail.com>
	<CABEEk167VTaivOLa9AY5xYLAEcpYRm9w+09jFPKLfy=x53D0sw@mail.gmail.com>
	<Pine.LNX.4.64.1501231422550.2125@agrippa.bic.mni.mcgill.ca>
	<CABApf9Hy4X-YCgY9MuC-Pg9cExGnYsEURZrEeQEBjgU-ELFZKQ@mail.gmail.com>
	<CAMCwi7Mn5M1vbH3r64cZnQpVVi553dSpRKhYAcPhL64xhuicqw@mail.gmail.com>
Message-ID: <CABEEk15cv6bGCo0YOSOi643+maabVJU74nr9vk7OscBYQi=z8w@mail.gmail.com>

Hi Vladimir,

Definitely not - ILT should be part of MINC and friends. It's used by
CIVET, but that's about it, much like CIVET uses mincmath.

-- A

On Fri, Jan 23, 2015 at 2:49 PM, Vladimir S. FONOV <vladimir.fonov at gmail.com
> wrote:

> Isn't it all part of CIVET?  Then Claude will be the one maintaining it.
>
>
> On Fri, Jan 23, 2015 at 2:46 PM, Andrew Wood <andrew at biospective.com>
> wrote:
>
> > Hi all,
> >
> > Alex's images are really easy to make with the create_verify_image script
> > that we're running here at Biospective. We've added quite a number of
> > convenience functions (e.g. on-the-fly marching_cubes for surface
> overlays,
> > thresholding options for volume overlays, etc).
> >
> > His PET to T1 image would be made with a call like this:
> > $ create_verify_image PET2T1_stx.png  \
> > -autocols 4 -width 2400 \
> > -row t1_stx.mnc color:gray surface_overylay:csf_stx.mnc:blue \
> > -row PET_stx.mnc color:gray surface_overylay:csf_stx.mnc:blue
> >
> > Does anyone know where the ILT source code lives, and who is maintaining
> > it? It'd be great if we could feed these improvements back to the
> > community.
> >
> > Best,
> > Andrew
> >
> > On Fri, Jan 23, 2015 at 2:24 PM, Paul GRAVEL <pgravel at bic.mni.mcgill.ca>
> > wrote:
> >
> > > Thanks also Alex and Andrew!
> > > Alex, very nice images!
> > > I will look into using this tool more closely.
> > > Best,
> > > Paul
> > >
> > >
> > >
> > > On Tue, 20 Jan 2015, Alex Zijdenbos wrote:
> > >
> > >  Or you can use create_verify_image (bundled with ILT), and pretty
> simply
> > >> create images like these:
> > >>
> > >> PET to T1 <https://dl.dropboxusercontent.com/u/
> > >> 5709165/MINC/PET2T1_stx.png>
> > >> PET stx <https://dl.dropboxusercontent.com/u/5709165/MINC/PET_stx.png
> >
> > >>
> > >> -- A
> > >>
> > >>
> > >> On Tue, Jan 20, 2015 at 6:44 PM, Andrew Janke <a.janke at gmail.com>
> > wrote:
> > >>
> > >>  Claude and Vladimir's suggestions will certainly do what you are
> > >>> requesting, but in case others are watching on, here is a somewhat
> > >>> easier way to achieve what Claude posted albeit with slightly less
> > >>> control on the chosen slice(s).
> > >>>
> > >>>    mincpik -triplanar -tilesize 300 -horizontal -title "bob the cat"
> > >>> input.mnc out.jpg
> > >>>
> > >>> If like me, you'd like a slice offset from the centre by 10% of the
> > >>> volume size in the sagittal direction then do this:
> > >>>
> > >>>    mincpik -triplanar -tilesize 300 -horizontal -title "bob the cat"
> > >>> -sagittal_offset_perc 10 input.mnc out.jpg
> > >>>
> > >>>
> > >>> a
> > >>>
> > >>> On 21 January 2015 at 06:31, Claude LEPAGE <claude at bic.mni.mcgill.ca
> >
> > >>> wrote:
> > >>>
> > >>>> Hi Paul,
> > >>>>
> > >>>> Try something like this, in Perlish way:
> > >>>>
> > >>>>   `mincpik -clobber -slice 100 -axial -width 300 -lookup -spectral
> > >>>>
> > >>> $input /tmp/axial.jpg`;
> > >>>
> > >>>>   `mincpik -clobber -slice 100 -coronal -width 300 -lookup -spectral
> > >>>>
> > >>> $input /tmp/coronal.jpg`;
> > >>>
> > >>>>   `mincpik -clobber -slice 100 -sagittal -width 300 -lookup
> -spectral
> > >>>>
> > >>> $input /tmp/sagittal.jpg`;
> > >>>
> > >>>>   `montage -tile 3x1 -background black -geometry 300x300+1+1
> > >>>>
> > >>> /tmp/axial.jpg /tmp/coronal.jpg /tmp/sagittal.jpg image_t1.jpg`;
> > >>>
> > >>>>
> > >>>> $input is you minc file in stx space. You can play with the
> > >>>> colour scheme if you don't like spectral.
> > >>>>
> > >>>> I do the above in a script when I convert from DICOM/nii to minc
> > >>>> in order to check the sanity of the minc files.
> > >>>>
> > >>>> 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
> > >>>
> > >>>
> > >>>  _______________________________________________
> > >> 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
> >
>
>
>
> --
> 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
>
>

From vladimir.fonov at gmail.com  Fri Jan 23 14:56:30 2015
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Fri, 23 Jan 2015 14:56:30 -0500
Subject: [MINC-users] Outputting overlay of co-registered MINC files
 directly to a file
In-Reply-To: <CABEEk15cv6bGCo0YOSOi643+maabVJU74nr9vk7OscBYQi=z8w@mail.gmail.com>
References: <Pine.LNX.4.64.1501201513190.8959@agrippa.bic.mni.mcgill.ca>
	<201501202031.t0KKVWZt011465@agrippa.bic.mni.mcgill.ca>
	<CAG0CB22kBZxmtWPt=QCTP3-wXVAfNnqF-gMbGeoYXXyhotyGzg@mail.gmail.com>
	<CABEEk167VTaivOLa9AY5xYLAEcpYRm9w+09jFPKLfy=x53D0sw@mail.gmail.com>
	<Pine.LNX.4.64.1501231422550.2125@agrippa.bic.mni.mcgill.ca>
	<CABApf9Hy4X-YCgY9MuC-Pg9cExGnYsEURZrEeQEBjgU-ELFZKQ@mail.gmail.com>
	<CAMCwi7Mn5M1vbH3r64cZnQpVVi553dSpRKhYAcPhL64xhuicqw@mail.gmail.com>
	<CABEEk15cv6bGCo0YOSOi643+maabVJU74nr9vk7OscBYQi=z8w@mail.gmail.com>
Message-ID: <CAMCwi7O77c0MvRiTL6P2r-FWODfiYuH4ACKnsxhf-VpwWbvLgA@mail.gmail.com>

Ok, I see it on cvs.bic.mni.mcgill.ca
Does it mean that i can transfer it to the github ?

On Fri, Jan 23, 2015 at 2:53 PM, Alex Zijdenbos <zijdenbos at gmail.com> wrote:

> Hi Vladimir,
>
> Definitely not - ILT should be part of MINC and friends. It's used by
> CIVET, but that's about it, much like CIVET uses mincmath.
>
> -- A
>
> On Fri, Jan 23, 2015 at 2:49 PM, Vladimir S. FONOV <
> vladimir.fonov at gmail.com
> > wrote:
>
> > Isn't it all part of CIVET?  Then Claude will be the one maintaining it.
> >
> >
> > On Fri, Jan 23, 2015 at 2:46 PM, Andrew Wood <andrew at biospective.com>
> > wrote:
> >
> > > Hi all,
> > >
> > > Alex's images are really easy to make with the create_verify_image
> script
> > > that we're running here at Biospective. We've added quite a number of
> > > convenience functions (e.g. on-the-fly marching_cubes for surface
> > overlays,
> > > thresholding options for volume overlays, etc).
> > >
> > > His PET to T1 image would be made with a call like this:
> > > $ create_verify_image PET2T1_stx.png  \
> > > -autocols 4 -width 2400 \
> > > -row t1_stx.mnc color:gray surface_overylay:csf_stx.mnc:blue \
> > > -row PET_stx.mnc color:gray surface_overylay:csf_stx.mnc:blue
> > >
> > > Does anyone know where the ILT source code lives, and who is
> maintaining
> > > it? It'd be great if we could feed these improvements back to the
> > > community.
> > >
> > > Best,
> > > Andrew
> > >
> > > On Fri, Jan 23, 2015 at 2:24 PM, Paul GRAVEL <
> pgravel at bic.mni.mcgill.ca>
> > > wrote:
> > >
> > > > Thanks also Alex and Andrew!
> > > > Alex, very nice images!
> > > > I will look into using this tool more closely.
> > > > Best,
> > > > Paul
> > > >
> > > >
> > > >
> > > > On Tue, 20 Jan 2015, Alex Zijdenbos wrote:
> > > >
> > > >  Or you can use create_verify_image (bundled with ILT), and pretty
> > simply
> > > >> create images like these:
> > > >>
> > > >> PET to T1 <https://dl.dropboxusercontent.com/u/
> > > >> 5709165/MINC/PET2T1_stx.png>
> > > >> PET stx <
> https://dl.dropboxusercontent.com/u/5709165/MINC/PET_stx.png
> > >
> > > >>
> > > >> -- A
> > > >>
> > > >>
> > > >> On Tue, Jan 20, 2015 at 6:44 PM, Andrew Janke <a.janke at gmail.com>
> > > wrote:
> > > >>
> > > >>  Claude and Vladimir's suggestions will certainly do what you are
> > > >>> requesting, but in case others are watching on, here is a somewhat
> > > >>> easier way to achieve what Claude posted albeit with slightly less
> > > >>> control on the chosen slice(s).
> > > >>>
> > > >>>    mincpik -triplanar -tilesize 300 -horizontal -title "bob the
> cat"
> > > >>> input.mnc out.jpg
> > > >>>
> > > >>> If like me, you'd like a slice offset from the centre by 10% of the
> > > >>> volume size in the sagittal direction then do this:
> > > >>>
> > > >>>    mincpik -triplanar -tilesize 300 -horizontal -title "bob the
> cat"
> > > >>> -sagittal_offset_perc 10 input.mnc out.jpg
> > > >>>
> > > >>>
> > > >>> a
> > > >>>
> > > >>> On 21 January 2015 at 06:31, Claude LEPAGE <
> claude at bic.mni.mcgill.ca
> > >
> > > >>> wrote:
> > > >>>
> > > >>>> Hi Paul,
> > > >>>>
> > > >>>> Try something like this, in Perlish way:
> > > >>>>
> > > >>>>   `mincpik -clobber -slice 100 -axial -width 300 -lookup -spectral
> > > >>>>
> > > >>> $input /tmp/axial.jpg`;
> > > >>>
> > > >>>>   `mincpik -clobber -slice 100 -coronal -width 300 -lookup
> -spectral
> > > >>>>
> > > >>> $input /tmp/coronal.jpg`;
> > > >>>
> > > >>>>   `mincpik -clobber -slice 100 -sagittal -width 300 -lookup
> > -spectral
> > > >>>>
> > > >>> $input /tmp/sagittal.jpg`;
> > > >>>
> > > >>>>   `montage -tile 3x1 -background black -geometry 300x300+1+1
> > > >>>>
> > > >>> /tmp/axial.jpg /tmp/coronal.jpg /tmp/sagittal.jpg image_t1.jpg`;
> > > >>>
> > > >>>>
> > > >>>> $input is you minc file in stx space. You can play with the
> > > >>>> colour scheme if you don't like spectral.
> > > >>>>
> > > >>>> I do the above in a script when I convert from DICOM/nii to minc
> > > >>>> in order to check the sanity of the minc files.
> > > >>>>
> > > >>>> 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
> > > >>>
> > > >>>
> > > >>>  _______________________________________________
> > > >> 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
> > >
> >
> >
> >
> > --
> > 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
> >
> >
> _______________________________________________
> 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

From zijdenbos at gmail.com  Fri Jan 23 15:11:37 2015
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Fri, 23 Jan 2015 15:11:37 -0500
Subject: [MINC-users] Outputting overlay of co-registered MINC files
 directly to a file
In-Reply-To: <CAMCwi7O77c0MvRiTL6P2r-FWODfiYuH4ACKnsxhf-VpwWbvLgA@mail.gmail.com>
References: <Pine.LNX.4.64.1501201513190.8959@agrippa.bic.mni.mcgill.ca>
	<201501202031.t0KKVWZt011465@agrippa.bic.mni.mcgill.ca>
	<CAG0CB22kBZxmtWPt=QCTP3-wXVAfNnqF-gMbGeoYXXyhotyGzg@mail.gmail.com>
	<CABEEk167VTaivOLa9AY5xYLAEcpYRm9w+09jFPKLfy=x53D0sw@mail.gmail.com>
	<Pine.LNX.4.64.1501231422550.2125@agrippa.bic.mni.mcgill.ca>
	<CABApf9Hy4X-YCgY9MuC-Pg9cExGnYsEURZrEeQEBjgU-ELFZKQ@mail.gmail.com>
	<CAMCwi7Mn5M1vbH3r64cZnQpVVi553dSpRKhYAcPhL64xhuicqw@mail.gmail.com>
	<CABEEk15cv6bGCo0YOSOi643+maabVJU74nr9vk7OscBYQi=z8w@mail.gmail.com>
	<CAMCwi7O77c0MvRiTL6P2r-FWODfiYuH4ACKnsxhf-VpwWbvLgA@mail.gmail.com>
Message-ID: <CABEEk16jtN331DNa6Gv=ka0e6SxJug7HKhVbp4K4gM18FtDNYw@mail.gmail.com>

I'd say so. It's been available forever - I actually always assumed it was
on github :)

For those who are wondering, ILT stands for Image Layout Toolkit. It was
written by David MacDonald as a generic perl library for creating
verification images. create_verify_image is the main script that lets you
generate images of the kind I sent along; typically, you define
cross-sections through a volume horizontally, and add rows of images with
overlays and etc vertically.

-- A

On Fri, Jan 23, 2015 at 2:56 PM, Vladimir S. FONOV <vladimir.fonov at gmail.com
> wrote:

> Ok, I see it on cvs.bic.mni.mcgill.ca
> Does it mean that i can transfer it to the github ?
>
> On Fri, Jan 23, 2015 at 2:53 PM, Alex Zijdenbos <zijdenbos at gmail.com>
> wrote:
>
> > Hi Vladimir,
> >
> > Definitely not - ILT should be part of MINC and friends. It's used by
> > CIVET, but that's about it, much like CIVET uses mincmath.
> >
> > -- A
> >
> > On Fri, Jan 23, 2015 at 2:49 PM, Vladimir S. FONOV <
> > vladimir.fonov at gmail.com
> > > wrote:
> >
> > > Isn't it all part of CIVET?  Then Claude will be the one maintaining
> it.
> > >
> > >
> > > On Fri, Jan 23, 2015 at 2:46 PM, Andrew Wood <andrew at biospective.com>
> > > wrote:
> > >
> > > > Hi all,
> > > >
> > > > Alex's images are really easy to make with the create_verify_image
> > script
> > > > that we're running here at Biospective. We've added quite a number of
> > > > convenience functions (e.g. on-the-fly marching_cubes for surface
> > > overlays,
> > > > thresholding options for volume overlays, etc).
> > > >
> > > > His PET to T1 image would be made with a call like this:
> > > > $ create_verify_image PET2T1_stx.png  \
> > > > -autocols 4 -width 2400 \
> > > > -row t1_stx.mnc color:gray surface_overylay:csf_stx.mnc:blue \
> > > > -row PET_stx.mnc color:gray surface_overylay:csf_stx.mnc:blue
> > > >
> > > > Does anyone know where the ILT source code lives, and who is
> > maintaining
> > > > it? It'd be great if we could feed these improvements back to the
> > > > community.
> > > >
> > > > Best,
> > > > Andrew
> > > >
> > > > On Fri, Jan 23, 2015 at 2:24 PM, Paul GRAVEL <
> > pgravel at bic.mni.mcgill.ca>
> > > > wrote:
> > > >
> > > > > Thanks also Alex and Andrew!
> > > > > Alex, very nice images!
> > > > > I will look into using this tool more closely.
> > > > > Best,
> > > > > Paul
> > > > >
> > > > >
> > > > >
> > > > > On Tue, 20 Jan 2015, Alex Zijdenbos wrote:
> > > > >
> > > > >  Or you can use create_verify_image (bundled with ILT), and pretty
> > > simply
> > > > >> create images like these:
> > > > >>
> > > > >> PET to T1 <https://dl.dropboxusercontent.com/u/
> > > > >> 5709165/MINC/PET2T1_stx.png>
> > > > >> PET stx <
> > https://dl.dropboxusercontent.com/u/5709165/MINC/PET_stx.png
> > > >
> > > > >>
> > > > >> -- A
> > > > >>
> > > > >>
> > > > >> On Tue, Jan 20, 2015 at 6:44 PM, Andrew Janke <a.janke at gmail.com>
> > > > wrote:
> > > > >>
> > > > >>  Claude and Vladimir's suggestions will certainly do what you are
> > > > >>> requesting, but in case others are watching on, here is a
> somewhat
> > > > >>> easier way to achieve what Claude posted albeit with slightly
> less
> > > > >>> control on the chosen slice(s).
> > > > >>>
> > > > >>>    mincpik -triplanar -tilesize 300 -horizontal -title "bob the
> > cat"
> > > > >>> input.mnc out.jpg
> > > > >>>
> > > > >>> If like me, you'd like a slice offset from the centre by 10% of
> the
> > > > >>> volume size in the sagittal direction then do this:
> > > > >>>
> > > > >>>    mincpik -triplanar -tilesize 300 -horizontal -title "bob the
> > cat"
> > > > >>> -sagittal_offset_perc 10 input.mnc out.jpg
> > > > >>>
> > > > >>>
> > > > >>> a
> > > > >>>
> > > > >>> On 21 January 2015 at 06:31, Claude LEPAGE <
> > claude at bic.mni.mcgill.ca
> > > >
> > > > >>> wrote:
> > > > >>>
> > > > >>>> Hi Paul,
> > > > >>>>
> > > > >>>> Try something like this, in Perlish way:
> > > > >>>>
> > > > >>>>   `mincpik -clobber -slice 100 -axial -width 300 -lookup
> -spectral
> > > > >>>>
> > > > >>> $input /tmp/axial.jpg`;
> > > > >>>
> > > > >>>>   `mincpik -clobber -slice 100 -coronal -width 300 -lookup
> > -spectral
> > > > >>>>
> > > > >>> $input /tmp/coronal.jpg`;
> > > > >>>
> > > > >>>>   `mincpik -clobber -slice 100 -sagittal -width 300 -lookup
> > > -spectral
> > > > >>>>
> > > > >>> $input /tmp/sagittal.jpg`;
> > > > >>>
> > > > >>>>   `montage -tile 3x1 -background black -geometry 300x300+1+1
> > > > >>>>
> > > > >>> /tmp/axial.jpg /tmp/coronal.jpg /tmp/sagittal.jpg image_t1.jpg`;
> > > > >>>
> > > > >>>>
> > > > >>>> $input is you minc file in stx space. You can play with the
> > > > >>>> colour scheme if you don't like spectral.
> > > > >>>>
> > > > >>>> I do the above in a script when I convert from DICOM/nii to minc
> > > > >>>> in order to check the sanity of the minc files.
> > > > >>>>
> > > > >>>> 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
> > > > >>>
> > > > >>>
> > > > >>>  _______________________________________________
> > > > >> 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
> > > >
> > >
> > >
> > >
> > > --
> > > 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
> > >
> > >
> > _______________________________________________
> > 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
>
>

From a.janke at gmail.com  Fri Jan 23 15:22:35 2015
From: a.janke at gmail.com (Andrew Janke)
Date: Sat, 24 Jan 2015 06:22:35 +1000
Subject: [MINC-users] Outputting overlay of co-registered MINC files
 directly to a file
In-Reply-To: <CAMCwi7O77c0MvRiTL6P2r-FWODfiYuH4ACKnsxhf-VpwWbvLgA@mail.gmail.com>
References: <Pine.LNX.4.64.1501201513190.8959@agrippa.bic.mni.mcgill.ca>
	<201501202031.t0KKVWZt011465@agrippa.bic.mni.mcgill.ca>
	<CAG0CB22kBZxmtWPt=QCTP3-wXVAfNnqF-gMbGeoYXXyhotyGzg@mail.gmail.com>
	<CABEEk167VTaivOLa9AY5xYLAEcpYRm9w+09jFPKLfy=x53D0sw@mail.gmail.com>
	<Pine.LNX.4.64.1501231422550.2125@agrippa.bic.mni.mcgill.ca>
	<CABApf9Hy4X-YCgY9MuC-Pg9cExGnYsEURZrEeQEBjgU-ELFZKQ@mail.gmail.com>
	<CAMCwi7Mn5M1vbH3r64cZnQpVVi553dSpRKhYAcPhL64xhuicqw@mail.gmail.com>
	<CABEEk15cv6bGCo0YOSOi643+maabVJU74nr9vk7OscBYQi=z8w@mail.gmail.com>
	<CAMCwi7O77c0MvRiTL6P2r-FWODfiYuH4ACKnsxhf-VpwWbvLgA@mail.gmail.com>
Message-ID: <CAG0CB23p17jQ2iqt2NWHFSvwkUQX7cuV-CuZKtRAMyDq1G-f9w@mail.gmail.com>

it's on packages in the tgz directory.

a
On 24/01/2015 5:57 AM, "Vladimir S. FONOV" <vladimir.fonov at gmail.com> wrote:

> Ok, I see it on cvs.bic.mni.mcgill.ca
> Does it mean that i can transfer it to the github ?
>
> On Fri, Jan 23, 2015 at 2:53 PM, Alex Zijdenbos <zijdenbos at gmail.com>
> wrote:
>
> > Hi Vladimir,
> >
> > Definitely not - ILT should be part of MINC and friends. It's used by
> > CIVET, but that's about it, much like CIVET uses mincmath.
> >
> > -- A
> >
> > On Fri, Jan 23, 2015 at 2:49 PM, Vladimir S. FONOV <
> > vladimir.fonov at gmail.com
> > > wrote:
> >
> > > Isn't it all part of CIVET?  Then Claude will be the one maintaining
> it.
> > >
> > >
> > > On Fri, Jan 23, 2015 at 2:46 PM, Andrew Wood <andrew at biospective.com>
> > > wrote:
> > >
> > > > Hi all,
> > > >
> > > > Alex's images are really easy to make with the create_verify_image
> > script
> > > > that we're running here at Biospective. We've added quite a number of
> > > > convenience functions (e.g. on-the-fly marching_cubes for surface
> > > overlays,
> > > > thresholding options for volume overlays, etc).
> > > >
> > > > His PET to T1 image would be made with a call like this:
> > > > $ create_verify_image PET2T1_stx.png  \
> > > > -autocols 4 -width 2400 \
> > > > -row t1_stx.mnc color:gray surface_overylay:csf_stx.mnc:blue \
> > > > -row PET_stx.mnc color:gray surface_overylay:csf_stx.mnc:blue
> > > >
> > > > Does anyone know where the ILT source code lives, and who is
> > maintaining
> > > > it? It'd be great if we could feed these improvements back to the
> > > > community.
> > > >
> > > > Best,
> > > > Andrew
> > > >
> > > > On Fri, Jan 23, 2015 at 2:24 PM, Paul GRAVEL <
> > pgravel at bic.mni.mcgill.ca>
> > > > wrote:
> > > >
> > > > > Thanks also Alex and Andrew!
> > > > > Alex, very nice images!
> > > > > I will look into using this tool more closely.
> > > > > Best,
> > > > > Paul
> > > > >
> > > > >
> > > > >
> > > > > On Tue, 20 Jan 2015, Alex Zijdenbos wrote:
> > > > >
> > > > >  Or you can use create_verify_image (bundled with ILT), and pretty
> > > simply
> > > > >> create images like these:
> > > > >>
> > > > >> PET to T1 <https://dl.dropboxusercontent.com/u/
> > > > >> 5709165/MINC/PET2T1_stx.png>
> > > > >> PET stx <
> > https://dl.dropboxusercontent.com/u/5709165/MINC/PET_stx.png
> > > >
> > > > >>
> > > > >> -- A
> > > > >>
> > > > >>
> > > > >> On Tue, Jan 20, 2015 at 6:44 PM, Andrew Janke <a.janke at gmail.com>
> > > > wrote:
> > > > >>
> > > > >>  Claude and Vladimir's suggestions will certainly do what you are
> > > > >>> requesting, but in case others are watching on, here is a
> somewhat
> > > > >>> easier way to achieve what Claude posted albeit with slightly
> less
> > > > >>> control on the chosen slice(s).
> > > > >>>
> > > > >>>    mincpik -triplanar -tilesize 300 -horizontal -title "bob the
> > cat"
> > > > >>> input.mnc out.jpg
> > > > >>>
> > > > >>> If like me, you'd like a slice offset from the centre by 10% of
> the
> > > > >>> volume size in the sagittal direction then do this:
> > > > >>>
> > > > >>>    mincpik -triplanar -tilesize 300 -horizontal -title "bob the
> > cat"
> > > > >>> -sagittal_offset_perc 10 input.mnc out.jpg
> > > > >>>
> > > > >>>
> > > > >>> a
> > > > >>>
> > > > >>> On 21 January 2015 at 06:31, Claude LEPAGE <
> > claude at bic.mni.mcgill.ca
> > > >
> > > > >>> wrote:
> > > > >>>
> > > > >>>> Hi Paul,
> > > > >>>>
> > > > >>>> Try something like this, in Perlish way:
> > > > >>>>
> > > > >>>>   `mincpik -clobber -slice 100 -axial -width 300 -lookup
> -spectral
> > > > >>>>
> > > > >>> $input /tmp/axial.jpg`;
> > > > >>>
> > > > >>>>   `mincpik -clobber -slice 100 -coronal -width 300 -lookup
> > -spectral
> > > > >>>>
> > > > >>> $input /tmp/coronal.jpg`;
> > > > >>>
> > > > >>>>   `mincpik -clobber -slice 100 -sagittal -width 300 -lookup
> > > -spectral
> > > > >>>>
> > > > >>> $input /tmp/sagittal.jpg`;
> > > > >>>
> > > > >>>>   `montage -tile 3x1 -background black -geometry 300x300+1+1
> > > > >>>>
> > > > >>> /tmp/axial.jpg /tmp/coronal.jpg /tmp/sagittal.jpg image_t1.jpg`;
> > > > >>>
> > > > >>>>
> > > > >>>> $input is you minc file in stx space. You can play with the
> > > > >>>> colour scheme if you don't like spectral.
> > > > >>>>
> > > > >>>> I do the above in a script when I convert from DICOM/nii to minc
> > > > >>>> in order to check the sanity of the minc files.
> > > > >>>>
> > > > >>>> 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
> > > > >>>
> > > > >>>
> > > > >>>  _______________________________________________
> > > > >> 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
> > > >
> > >
> > >
> > >
> > > --
> > > 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
> > >
> > >
> > _______________________________________________
> > 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
>

From vladimir.fonov at gmail.com  Fri Jan 23 15:27:00 2015
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Fri, 23 Jan 2015 15:27:00 -0500
Subject: [MINC-users] Outputting overlay of co-registered MINC files
 directly to a file
In-Reply-To: <CAG0CB23p17jQ2iqt2NWHFSvwkUQX7cuV-CuZKtRAMyDq1G-f9w@mail.gmail.com>
References: <Pine.LNX.4.64.1501201513190.8959@agrippa.bic.mni.mcgill.ca>
	<201501202031.t0KKVWZt011465@agrippa.bic.mni.mcgill.ca>
	<CAG0CB22kBZxmtWPt=QCTP3-wXVAfNnqF-gMbGeoYXXyhotyGzg@mail.gmail.com>
	<CABEEk167VTaivOLa9AY5xYLAEcpYRm9w+09jFPKLfy=x53D0sw@mail.gmail.com>
	<Pine.LNX.4.64.1501231422550.2125@agrippa.bic.mni.mcgill.ca>
	<CABApf9Hy4X-YCgY9MuC-Pg9cExGnYsEURZrEeQEBjgU-ELFZKQ@mail.gmail.com>
	<CAMCwi7Mn5M1vbH3r64cZnQpVVi553dSpRKhYAcPhL64xhuicqw@mail.gmail.com>
	<CABEEk15cv6bGCo0YOSOi643+maabVJU74nr9vk7OscBYQi=z8w@mail.gmail.com>
	<CAMCwi7O77c0MvRiTL6P2r-FWODfiYuH4ACKnsxhf-VpwWbvLgA@mail.gmail.com>
	<CAG0CB23p17jQ2iqt2NWHFSvwkUQX7cuV-CuZKtRAMyDq1G-f9w@mail.gmail.com>
Message-ID: <CAMCwi7P=g=ZZhQ8_dS9JXy83J1wWKoGbwNHWzmRZ_d5tP5b0eQ@mail.gmail.com>

ok, it is here: https://github.com/BIC-MNI/ILT


On Fri, Jan 23, 2015 at 3:22 PM, Andrew Janke <a.janke at gmail.com> wrote:

> it's on packages in the tgz directory.
>
> a
> On 24/01/2015 5:57 AM, "Vladimir S. FONOV" <vladimir.fonov at gmail.com>
> wrote:
>
> > Ok, I see it on cvs.bic.mni.mcgill.ca
> > Does it mean that i can transfer it to the github ?
> >
> > On Fri, Jan 23, 2015 at 2:53 PM, Alex Zijdenbos <zijdenbos at gmail.com>
> > wrote:
> >
> > > Hi Vladimir,
> > >
> > > Definitely not - ILT should be part of MINC and friends. It's used by
> > > CIVET, but that's about it, much like CIVET uses mincmath.
> > >
> > > -- A
> > >
> > > On Fri, Jan 23, 2015 at 2:49 PM, Vladimir S. FONOV <
> > > vladimir.fonov at gmail.com
> > > > wrote:
> > >
> > > > Isn't it all part of CIVET?  Then Claude will be the one maintaining
> > it.
> > > >
> > > >
> > > > On Fri, Jan 23, 2015 at 2:46 PM, Andrew Wood <andrew at biospective.com
> >
> > > > wrote:
> > > >
> > > > > Hi all,
> > > > >
> > > > > Alex's images are really easy to make with the create_verify_image
> > > script
> > > > > that we're running here at Biospective. We've added quite a number
> of
> > > > > convenience functions (e.g. on-the-fly marching_cubes for surface
> > > > overlays,
> > > > > thresholding options for volume overlays, etc).
> > > > >
> > > > > His PET to T1 image would be made with a call like this:
> > > > > $ create_verify_image PET2T1_stx.png  \
> > > > > -autocols 4 -width 2400 \
> > > > > -row t1_stx.mnc color:gray surface_overylay:csf_stx.mnc:blue \
> > > > > -row PET_stx.mnc color:gray surface_overylay:csf_stx.mnc:blue
> > > > >
> > > > > Does anyone know where the ILT source code lives, and who is
> > > maintaining
> > > > > it? It'd be great if we could feed these improvements back to the
> > > > > community.
> > > > >
> > > > > Best,
> > > > > Andrew
> > > > >
> > > > > On Fri, Jan 23, 2015 at 2:24 PM, Paul GRAVEL <
> > > pgravel at bic.mni.mcgill.ca>
> > > > > wrote:
> > > > >
> > > > > > Thanks also Alex and Andrew!
> > > > > > Alex, very nice images!
> > > > > > I will look into using this tool more closely.
> > > > > > Best,
> > > > > > Paul
> > > > > >
> > > > > >
> > > > > >
> > > > > > On Tue, 20 Jan 2015, Alex Zijdenbos wrote:
> > > > > >
> > > > > >  Or you can use create_verify_image (bundled with ILT), and
> pretty
> > > > simply
> > > > > >> create images like these:
> > > > > >>
> > > > > >> PET to T1 <https://dl.dropboxusercontent.com/u/
> > > > > >> 5709165/MINC/PET2T1_stx.png>
> > > > > >> PET stx <
> > > https://dl.dropboxusercontent.com/u/5709165/MINC/PET_stx.png
> > > > >
> > > > > >>
> > > > > >> -- A
> > > > > >>
> > > > > >>
> > > > > >> On Tue, Jan 20, 2015 at 6:44 PM, Andrew Janke <
> a.janke at gmail.com>
> > > > > wrote:
> > > > > >>
> > > > > >>  Claude and Vladimir's suggestions will certainly do what you
> are
> > > > > >>> requesting, but in case others are watching on, here is a
> > somewhat
> > > > > >>> easier way to achieve what Claude posted albeit with slightly
> > less
> > > > > >>> control on the chosen slice(s).
> > > > > >>>
> > > > > >>>    mincpik -triplanar -tilesize 300 -horizontal -title "bob the
> > > cat"
> > > > > >>> input.mnc out.jpg
> > > > > >>>
> > > > > >>> If like me, you'd like a slice offset from the centre by 10% of
> > the
> > > > > >>> volume size in the sagittal direction then do this:
> > > > > >>>
> > > > > >>>    mincpik -triplanar -tilesize 300 -horizontal -title "bob the
> > > cat"
> > > > > >>> -sagittal_offset_perc 10 input.mnc out.jpg
> > > > > >>>
> > > > > >>>
> > > > > >>> a
> > > > > >>>
> > > > > >>> On 21 January 2015 at 06:31, Claude LEPAGE <
> > > claude at bic.mni.mcgill.ca
> > > > >
> > > > > >>> wrote:
> > > > > >>>
> > > > > >>>> Hi Paul,
> > > > > >>>>
> > > > > >>>> Try something like this, in Perlish way:
> > > > > >>>>
> > > > > >>>>   `mincpik -clobber -slice 100 -axial -width 300 -lookup
> > -spectral
> > > > > >>>>
> > > > > >>> $input /tmp/axial.jpg`;
> > > > > >>>
> > > > > >>>>   `mincpik -clobber -slice 100 -coronal -width 300 -lookup
> > > -spectral
> > > > > >>>>
> > > > > >>> $input /tmp/coronal.jpg`;
> > > > > >>>
> > > > > >>>>   `mincpik -clobber -slice 100 -sagittal -width 300 -lookup
> > > > -spectral
> > > > > >>>>
> > > > > >>> $input /tmp/sagittal.jpg`;
> > > > > >>>
> > > > > >>>>   `montage -tile 3x1 -background black -geometry 300x300+1+1
> > > > > >>>>
> > > > > >>> /tmp/axial.jpg /tmp/coronal.jpg /tmp/sagittal.jpg
> image_t1.jpg`;
> > > > > >>>
> > > > > >>>>
> > > > > >>>> $input is you minc file in stx space. You can play with the
> > > > > >>>> colour scheme if you don't like spectral.
> > > > > >>>>
> > > > > >>>> I do the above in a script when I convert from DICOM/nii to
> minc
> > > > > >>>> in order to check the sanity of the minc files.
> > > > > >>>>
> > > > > >>>> 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
> > > > > >>>
> > > > > >>>
> > > > > >>>  _______________________________________________
> > > > > >> 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
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > 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
> > > >
> > > >
> > > _______________________________________________
> > > 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
> >
> _______________________________________________
> 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

From philip.novosad at mail.mcgill.ca  Sat Jan 24 23:56:23 2015
From: philip.novosad at mail.mcgill.ca (Philip Novosad)
Date: Sun, 25 Jan 2015 04:56:23 +0000
Subject: [MINC-users] ICBM152 non-linear atlas: symmetric vs asymmetric
In-Reply-To: <B2DBACDEC3CCE64EB1853BA56C3CFB281A53BF@EXMBX2010-4.campus.MCGILL.CA>
References: <B2DBACDEC3CCE64EB1853BA56C3CFB281A53BF@EXMBX2010-4.campus.MCGILL.CA>
Message-ID: <B2DBACDEC3CCE64EB1853BA56C3CFB281A574C@EXMBX2010-4.campus.MCGILL.CA>

Hi all,

I'm looking for a bit of information regarding the ICBM152 non-linear atlases. From my very limited understanding, there is a max probability atlas available (that is used with ANIMAL) associated with the symmetric version (I think this is called the 'lobe atlas' on the BIC website). Is there also one for the asymmetric version?

Are these atlases (the labeled volumes; I have my hands on the mean shape images!) available anywhere? I have only been able to find, on the BIC website, the standard GM/WM/CSF labels, not the 'lobe atlas'. Lastly, is there any information available about how they were made? Any information would be greatly appreciated.

Best,
Phil

From vladimir.fonov at gmail.com  Sun Jan 25 00:26:03 2015
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Sun, 25 Jan 2015 00:26:03 -0500
Subject: [MINC-users] ICBM152 non-linear atlas: symmetric vs asymmetric
In-Reply-To: <B2DBACDEC3CCE64EB1853BA56C3CFB281A574C@EXMBX2010-4.campus.MCGILL.CA>
References: <B2DBACDEC3CCE64EB1853BA56C3CFB281A53BF@EXMBX2010-4.campus.MCGILL.CA>
	<B2DBACDEC3CCE64EB1853BA56C3CFB281A574C@EXMBX2010-4.campus.MCGILL.CA>
Message-ID: <DAE85EB2-1357-47EF-9761-DF3C7328E3E7@gmail.com>

Hello Phil,

the lobe atlas is include with MINC1/2 version of symmetric templates - it is stored in a format suitable for lobe_segment minc tool , and contain separate masks for gray matter and white matter structures. 


On Jan 24, 2015, at 11:56 PM, Philip Novosad <philip.novosad at mail.mcgill.ca> wrote:

> Hi all,
> 
> I'm looking for a bit of information regarding the ICBM152 non-linear atlases. From my very limited understanding, there is a max probability atlas available (that is used with ANIMAL) associated with the symmetric version (I think this is called the 'lobe atlas' on the BIC website). Is there also one for the asymmetric version?
> 
> Are these atlases (the labeled volumes; I have my hands on the mean shape images!) available anywhere? I have only been able to find, on the BIC website, the standard GM/WM/CSF labels, not the 'lobe atlas'. Lastly, is there any information available about how they were made? Any information would be greatly appreciated.
> 
> Best,
> Phil
> _______________________________________________
> 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





From gdevenyi at gmail.com  Wed Jan 28 17:33:56 2015
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Wed, 28 Jan 2015 17:33:56 -0500
Subject: [MINC-users] Isolated Spots in mincbeast masks?
Message-ID: <CAFQOoOo-1Mnzjn0-+_KjWogA869ZixeGY6YfgoiC+zTY1LN2Lg@mail.gmail.com>

Hi all,

I?m having some trouble with mincbeast producing masks with isolated spots,
despite using the -fill option when invoking. See attached screenshot of a
brain-mask overlay.

I would?ve expected that the mask would be expanded to encompass the
isolated mask component, is that not the case?

I invoked mincbeast with the following

mincbeast -clobber -verbose -fill -median -same_res -flip -conf
/opt/quarantine/resources/BEaST_libraries/combined/default.1mm.conf
/opt/quarantine/resources/BEaST_libraries/combined
preprocessed/OAS1_0019_MR1_mpr_n4_anon_sbj_111.n4correct.affine_register_masked.cutneckapply.beastnormalize.mnc
preprocessed/OAS1_0019_MR1_mpr_n4_anon_sbj_111.n4correct.affine_register_masked.cutneckapply.beastnormalize.beastmask.mnc

?
?Am I missing something or is this a bug??


-- 
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