From michel.audette at kitware.com  Mon May  2 14:12:15 2011
From: michel.audette at kitware.com (Michel Audette)
Date: Mon, 2 May 2011 14:12:15 -0400
Subject: [MINC-users] looking for an example of a mincmorph kernel file
Message-ID: <BANLkTikeZVY=0f3YNTqFw=PYNwOne1yiyQ@mail.gmail.com>

Dear minc users,

I'm looking to implement a new mincmorph kernel file that dilates and erodes
mostly along the x-axis. Is there a kernel file somewhere that I can modify
appropriately?

Best wishes,

Michel


-- 
Michel Audette, Ph.D.
R & D Engineer,
Kitware Inc.,
Chapel Hill, N.C.

From zijdenbos at gmail.com  Mon May  2 14:21:34 2011
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Mon, 2 May 2011 14:21:34 -0400
Subject: [MINC-users] looking for an example of a mincmorph kernel file
In-Reply-To: <BANLkTikeZVY=0f3YNTqFw=PYNwOne1yiyQ@mail.gmail.com>
References: <BANLkTikeZVY=0f3YNTqFw=PYNwOne1yiyQ@mail.gmail.com>
Message-ID: <48245EC820F449548E52DC7D87DEC4E9@gmail.com>

Hi Michel,

I wrote a simple kernel-generator some time ago. It only generates a spherical kernel, but it would be simple enough to modify it to a non-isotropic kernel. You can find it here:

http://dl.dropbox.com/u/5709165/make_mincmorph_kernel.pl

-- A

-- 
Alex Zijdenbos
Sent with Sparrow
On Monday, May 2, 2011 at 2:12 PM, Michel Audette wrote: 
> Dear minc users,
> 
> I'm looking to implement a new mincmorph kernel file that dilates and erodes
> mostly along the x-axis. Is there a kernel file somewhere that I can modify
> appropriately?
> 
> Best wishes,
> 
> Michel
> 
> 
> -- 
> Michel Audette, Ph.D.
> R & D Engineer,
> Kitware Inc.,
> Chapel Hill, N.C.
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> 

From michel.audette at kitware.com  Mon May  2 14:42:08 2011
From: michel.audette at kitware.com (Michel Audette)
Date: Mon, 2 May 2011 14:42:08 -0400
Subject: [MINC-users] looking for an example of a mincmorph kernel file
In-Reply-To: <48245EC820F449548E52DC7D87DEC4E9@gmail.com>
References: <BANLkTikeZVY=0f3YNTqFw=PYNwOne1yiyQ@mail.gmail.com>
	<48245EC820F449548E52DC7D87DEC4E9@gmail.com>
Message-ID: <BANLkTimKPMjC0P44TBFgS24Ahwmv+4BBqw@mail.gmail.com>

Hi Alex,

Cool! I'll keep that in mind. I managed to find an old discussion thread
involving Andrew Janke from 2007.
http://www.bic.mni.mcgill.ca/pipermail/minc-users/2007-November/001819.html

I've tweaked the example that he provided, after all.

I'm about to try it.

I will probably revisit your idea if that does not work as expected.

Best wishes,

Michel


On Mon, May 2, 2011 at 2:21 PM, Alex Zijdenbos <zijdenbos at gmail.com> wrote:

> Hi Michel,
>
> I wrote a simple kernel-generator some time ago. It only generates a
> spherical kernel, but it would be simple enough to modify it to a
> non-isotropic kernel. You can find it here:
>
> http://dl.dropbox.com/u/5709165/make_mincmorph_kernel.pl
>
> -- A
>
> --
> Alex Zijdenbos
> Sent with Sparrow
> On Monday, May 2, 2011 at 2:12 PM, Michel Audette wrote:
> > Dear minc users,
> >
> > I'm looking to implement a new mincmorph kernel file that dilates and
> erodes
> > mostly along the x-axis. Is there a kernel file somewhere that I can
> modify
> > appropriately?
> >
> > Best wishes,
> >
> > Michel
> >
> >
> > --
> > Michel Audette, Ph.D.
> > R & D Engineer,
> > Kitware Inc.,
> > Chapel Hill, N.C.
> > _______________________________________________
> > 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
>



-- 
Michel Audette, Ph.D.
R & D Engineer,
Kitware Inc.,
Chapel Hill, N.C.

From a.janke at gmail.com  Mon May  2 19:36:59 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 3 May 2011 09:36:59 +1000
Subject: [MINC-users] looking for an example of a mincmorph kernel file
In-Reply-To: <BANLkTimKPMjC0P44TBFgS24Ahwmv+4BBqw@mail.gmail.com>
References: <BANLkTikeZVY=0f3YNTqFw=PYNwOne1yiyQ@mail.gmail.com>
	<48245EC820F449548E52DC7D87DEC4E9@gmail.com>
	<BANLkTimKPMjC0P44TBFgS24Ahwmv+4BBqw@mail.gmail.com>
Message-ID: <BANLkTimhKOF1Yt-N1W5+H6cehti93zo3eQ@mail.gmail.com>

Good good,

I'm late to the party but if you want some more examples have a look here:

   https://github.com/andrewjanke/mincmorph/tree/master/kernels

a

On Tue, May 3, 2011 at 04:42, Michel Audette <michel.audette at kitware.com> wrote:
> Cool! I'll keep that in mind. I managed to find an old discussion thread
> involving Andrew Janke from 2007.
> http://www.bic.mni.mcgill.ca/pipermail/minc-users/2007-November/001819.html

From atipirne at stanford.edu  Thu May  5 20:17:12 2011
From: atipirne at stanford.edu (Aaryani Tipirneni)
Date: Thu, 5 May 2011 17:17:12 -0700 (PDT)
Subject: [MINC-users] dcm2mnc failed for cornol data set
In-Reply-To: <330190562.1154854.1304640803310.JavaMail.root@zm04.stanford.edu>
Message-ID: <1431872753.1154981.1304641032389.JavaMail.root@zm04.stanford.edu>

Hi Minc users,

  I work on coregistration stuff using minc tools. Initially I convert the images to mnc using dcm2mnc script. For some reason, dcm2mnc is not working good for coronal data set, all the three axes are being flipped and so the coregistration is failing. Could you please help me if anyone knows.

Thanks for your time!

From a.janke at gmail.com  Sun May  8 18:04:52 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Mon, 9 May 2011 08:04:52 +1000
Subject: [MINC-users] dcm2mnc failed for cornol data set
In-Reply-To: <1431872753.1154981.1304641032389.JavaMail.root@zm04.stanford.edu>
References: <330190562.1154854.1304640803310.JavaMail.root@zm04.stanford.edu>
	<1431872753.1154981.1304641032389.JavaMail.root@zm04.stanford.edu>
Message-ID: <BANLkTimShQDeb00YfXqx4jBnuBmqNwg22g@mail.gmail.com>

Hi,

On Fri, May 6, 2011 at 10:17, Aaryani Tipirneni <atipirne at stanford.edu> wrote:
> ?I work on coregistration stuff using minc tools. Initially I convert the images to mnc using dcm2mnc script. For some reason, dcm2mnc is not working good for coronal data set, all the three axes are being flipped and so the coregistration is failing. Could you please help me if anyone knows.

These orientation issues are difficult to sort out unless we know
where and from what type of scanner your data is from.  In some cases
the DICOM headers themselves are "wrong".

In the meantime you can find volrot (rotate a volume) and volflip
(flip a volume along an axis) here:

   http://packages.bic.mni.mcgill.ca/scripts/


a

From pgravel at bic.mni.mcgill.ca  Tue May 10 12:01:07 2011
From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL)
Date: Tue, 10 May 2011 12:01:07 -0400 (EDT)
Subject: [MINC-users] Referencing MINC Tools
In-Reply-To: <BANLkTimShQDeb00YfXqx4jBnuBmqNwg22g@mail.gmail.com>
References: <330190562.1154854.1304640803310.JavaMail.root@zm04.stanford.edu>
	<1431872753.1154981.1304641032389.JavaMail.root@zm04.stanford.edu>
	<BANLkTimShQDeb00YfXqx4jBnuBmqNwg22g@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.1105101159390.29960@cassio.bic.mni.mcgill.ca>

Dear All,

I want to mention that I am using the MINC tools in a paper, and I was 
wondering what should I put as the reference?

Many thanks!

Paul



From atipirne at stanford.edu  Tue May 10 12:31:04 2011
From: atipirne at stanford.edu (Aaryani Tipirneni)
Date: Tue, 10 May 2011 09:31:04 -0700 (PDT)
Subject: [MINC-users] dcm2mnc failed for cornol data set
In-Reply-To: <BANLkTimShQDeb00YfXqx4jBnuBmqNwg22g@mail.gmail.com>
Message-ID: <1065346452.77834.1305045064988.JavaMail.root@zm04.stanford.edu>

Hi Andrew,

 Thank you so much. I'll try to flip and see the how the results will be.

Many Thanks!
Aaryani

----- Original Message -----
From: "Andrew Janke" <a.janke at gmail.com>
To: "MINC users mailing list" <minc-users at bic.mni.mcgill.ca>
Sent: Sunday, May 8, 2011 3:04:52 PM
Subject: Re: [MINC-users] dcm2mnc failed for cornol data set

Hi,

On Fri, May 6, 2011 at 10:17, Aaryani Tipirneni <atipirne at stanford.edu> wrote:
> ?I work on coregistration stuff using minc tools. Initially I convert the images to mnc using dcm2mnc script. For some reason, dcm2mnc is not working good for coronal data set, all the three axes are being flipped and so the coregistration is failing. Could you please help me if anyone knows.

These orientation issues are difficult to sort out unless we know
where and from what type of scanner your data is from.  In some cases
the DICOM headers themselves are "wrong".

In the meantime you can find volrot (rotate a volume) and volflip
(flip a volume along an axis) here:

   http://packages.bic.mni.mcgill.ca/scripts/


a
_______________________________________________
MINC-users at bic.mni.mcgill.ca
http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From a.janke at gmail.com  Fri May 13 01:08:29 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Fri, 13 May 2011 15:08:29 +1000
Subject: [MINC-users] Referencing MINC Tools
In-Reply-To: <Pine.LNX.4.64.1105101159390.29960@cassio.bic.mni.mcgill.ca>
References: <330190562.1154854.1304640803310.JavaMail.root@zm04.stanford.edu>
	<1431872753.1154981.1304641032389.JavaMail.root@zm04.stanford.edu>
	<BANLkTimShQDeb00YfXqx4jBnuBmqNwg22g@mail.gmail.com>
	<Pine.LNX.4.64.1105101159390.29960@cassio.bic.mni.mcgill.ca>
Message-ID: <BANLkTi=W9VJSsyaGmD=YdTFrX05JrzsyOQ@mail.gmail.com>

Hi Paul,

There is no canonical paper as "MINC" encapsulates a lot of things. My
general suggestion for this is to reference one of these two websites:

   http://www.bic.mni.mcgill.ca/ServicesSoftware/MINC
   http://en.wikibooks.org/wiki/MINC

Both should be fairly stable, although the 2nd perhaps slightly more so.


a

From MKeaser at umaryland.edu  Fri May 20 14:32:35 2011
From: MKeaser at umaryland.edu (Keaser, Michael L)
Date: Fri, 20 May 2011 14:32:35 -0400
Subject: [MINC-users] build almost everything minc Makefile and git
 repository for EZminc
In-Reply-To: <BANLkTikmohrVn0EKbvzZ535hOwekRDX8Ow@mail.gmail.com>
References: <4D715D1D.1090404@gmail.com>
	<00EF2C3B391AF84C8ED343F4469D4D56055F5BC2AB@UMBEXMBX2.campus.umaryland.edu>
	<AANLkTik1_N7tJRX2xJtEK8XL66uxrhMdY9Ti-Ac3piiB@mail.gmail.com>
	<00EF2C3B391AF84C8ED343F4469D4D56055F5BC2AC@UMBEXMBX2.campus.umaryland.edu>
	<AANLkTikkJqq6-5vqjjh4XXS9weKGP+UMx8p116Vsjz-d@mail.gmail.com>
	<AANLkTikeG=aYEP4k4weRZbAtB9r50Wekz7aw5+FHU=D7@mail.gmail.com>
	<00EF2C3B391AF84C8ED343F4469D4D56055F5BC2CE@UMBEXMBX2.campus.umaryland.edu>
	<BANLkTi=4kUd2TvC0w3OGvcBqgva03P0mrQ@mail.gmail.com>
	<BANLkTimyZV9Gtc5GOaPNq8RAz61Mt8fc5w@mail.gmail.com>
	<00EF2C3B391AF84C8ED343F4469D4D56055F5BC2D2@UMBEXMBX2.campus.umaryland.edu>
	<BANLkTinY-+2bHvHFTz0z3S6ZkzpkgN4qnQ@mail.gmail.com>
	<00EF2C3B391AF84C8ED343F4469D4D56055F5BC2D3@UMBEXMBX2.campus.umaryland.edu>
	<BANLkTikH2G3KgoNL_nPaMqWD1bAOVi0jyA@mail.gmail.com>
	<00EF2C3B391AF84C8ED343F4469D4D56055F5BC2D8@UMBEXMBX2.campus.umaryland.edu>
	<4D9DD5F0.3020002@gmail.com>
	<00EF2C3B391AF84C8ED343F4469D4D56055F5BC2DC@UMBEXMBX2.campus.umaryland.edu>,
	<BANLkTikmohrVn0EKbvzZ535hOwekRDX8Ow@mail.gmail.com>
Message-ID: <00EF2C3B391AF84C8ED343F4469D4D5605619D9F16@UMBEXMBX2.campus.umaryland.edu>

Hello,

Okay, I  tried that with this command line:

 gcc  -g -O2  -L/usr/local/minc/lib -lnetpbm -o Display dummy.o main/main.o main/display.o main/event_loop.o main/graphics.o main/three_d.o main/transforms.o atlas/atlas.o input_files/input_files.o input_files/volume_file.o callbacks/atlas.o callbacks/call_globals.o callbacks/colour_coding.o callbacks/file.o callbacks/line_ops.o callbacks/object_ops.o callbacks/marker_ops.o callbacks/polygon_ops.o callbacks/quit.o callbacks/regions.o callbacks/render_ops.o callbacks/segmenting.o callbacks/surf_segmenting.o callbacks/surface_curves.o callbacks/surface_extract.o callbacks/view_ops.o callbacks/volume_ops.o callbacks/volume_transform_ops.o current_obj/current_obj.o edit_surface/connected.o edit_surface/edit.o edit_surface/segment.o images/images.o markers/markers.o surface_extraction/boundary_extraction.o surface_extraction/data_structs.o surface_extraction/init_surface.o surface_extraction/extract.o surface_extraction/surface.o surface_extraction/surface_events.o voxel_scan/scan_objects.o events/change_markers.o events/clip_plane.o events/film_loop.o events/magnify.o events/mouse.o events/mouse_trans.o events/pick_object.o events/pick_view.o events/rotate_slice.o events/spaceball.o events/virt_sb.o events/window_man.o events/utilities.o immediate_mode/draw_immed.o intersect/ray_polygons.o intersect/plane_polygons.o cursor/cursor.o cursor/cursor_icon.o menu/build_menu.o menu/cursor_pos.o menu/menu.o menu/input_menu.o menu/selected.o menu/text.o cursor_contours/contours.o segmenting/cut_neighbours.o segmenting/painting.o segmenting/segmenting.o segmenting/segment_polygons.o slice_window/colour_bar.o slice_window/colour_coding.o slice_window/crop.o slice_window/draw_slice.o slice_window/histogram.o slice_window/pick_angle.o slice_window/quadmesh.o slice_window/slice.o slice_window/slice_3d.o slice_window/slice_events.o slice_window/undo.o slice_window/view.o surface_curves/closest_line.o surface_curves/events.o surface_curves/edge_distance.o tubes/convert_lines.o structures/action_table.o structures/fit_view.o structures/lights.o structures/render.o structures/view.o structures/window.o  Graphics/libbicgl.a -lGL  -lm -lGLU -lGL  -lm -lglut  -lSM -lICE -lXmu -lXi  -lGLU -lGL  -lm  -lpbm -lbicpl -lvolume_io2 -lminc2 -lhdf5 -lz -lnetcdf -lm -lm   -lbicpl -lvolume_io2 -lminc2 -lhdf5 -lz -lnetcdf -lm -lm

I still get this error message


/usr/local/minc/src/Display-1.5.0/slice_window/crop.c:165: warning: the use of `tmpnam' is dangerous, better use `mkstemp'
/usr/local/minc/lib/libbicpl.a(rgb_io.o): In function `output_rgb_file':
/usr/local/minc/src/bicpl-1.4.6/Images/rgb_io_ppm.c:95: undefined reference to `ppm_writeppminit'
/usr/local/minc/src/bicpl-1.4.6/Images/rgb_io_ppm.c:98: undefined reference to `ppm_allocrow'
/usr/local/minc/src/bicpl-1.4.6/Images/rgb_io_ppm.c:116: undefined reference to `ppm_writeppmrow'
/usr/local/minc/lib/libbicpl.a(rgb_io.o): In function `input_rgb_file':
/usr/local/minc/src/bicpl-1.4.6/Images/rgb_io_ppm.c:29: undefined reference to `ppm_readppminit'
/usr/local/minc/src/bicpl-1.4.6/Images/rgb_io_ppm.c:31: undefined reference to `ppm_allocrow'
/usr/local/minc/src/bicpl-1.4.6/Images/rgb_io_ppm.c:44: undefined reference to `ppm_readppmrow'
collect2: ld returned 1 exit status


Michael
________________________________________
From: minc-users-bounces at bic.mni.mcgill.ca [minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Vladimir S. FONOV [vladimir.fonov at gmail.com]
Sent: Thursday, April 07, 2011 11:59 AM
To: MINC users mailing list
Subject: Re: [MINC-users] build almost everything minc Makefile and git repository for EZminc

Hello,

then you should link with netpbm! I.e -L/usr/local/minc/lib -lnetpbm .

Probably you also have another version of pbm installed in the system
and something somewhere got confused.

On Thu, Apr 7, 2011 at 11:49 AM, Keaser, Michael L
<MKeaser at umaryland.edu> wrote:
> Valdimir,
>
>
> Yes, libnetpbm.a is in my /usr/local/minc/lib/ directory. So, i take it that means I link with netpbm. If I try using "lpbm", I get a similar error message.
>
> /usr/local/minc/src/Display-1.5.0/slice_window/crop.c:165: warning: the use of `tmpnam' is dangerous, better use `mkstemp'
> /usr/local/minc/lib/libbicpl.a(rgb_io.o): In function `output_rgb_file':
> /usr/local/minc/src/bicpl-1.4.6/Images/rgb_io_ppm.c:95: undefined reference to `ppm_writeppminit'
> /usr/local/minc/src/bicpl-1.4.6/Images/rgb_io_ppm.c:98: undefined reference to `ppm_allocrow'
> /usr/local/minc/src/bicpl-1.4.6/Images/rgb_io_ppm.c:116: undefined reference to `ppm_writeppmrow'
> /usr/local/minc/lib/libbicpl.a(rgb_io.o): In function `input_rgb_file':
> /usr/local/minc/src/bicpl-1.4.6/Images/rgb_io_ppm.c:29: undefined reference to `ppm_readppminit'
> /usr/local/minc/src/bicpl-1.4.6/Images/rgb_io_ppm.c:31: undefined reference to `ppm_allocrow'
> /usr/local/minc/src/bicpl-1.4.6/Images/rgb_io_ppm.c:44: undefined reference to `ppm_readppmrow'
> collect2: ld returned 1 exit status
>
>
> Michael
> ________________________________________
> From: minc-users-bounces at bic.mni.mcgill.ca [minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Vladimir S. FONOV [vladimir.fonov at gmail.com]
> Sent: Thursday, April 07, 2011 11:19 AM
> To: MINC users mailing list
> Subject: Re: [MINC-users] build almost everything minc Makefile and git repository for EZminc
>
> Hello,
>
> netpbm version 10.35.74 is build  as part of quarantine creation. There
> should be file libnetpbm.a in /usr/local/minc/lib
>
> Keaser, Michael L wrote:
>> Andrew,
>>
>> So are you saying substitute -lpgm -lpbm for the lppm? If so, when I did that, I received this message:
>>
>> /usr/local/minc/src/Display-1.5.0/slice_window/crop.c:165: warning: the use of `tmpnam' is dangerous, better use `mkstemp'
>> /usr/local/minc/lib/libbicpl.a(rgb_io.o): In function `output_rgb_file':
>> /usr/local/minc/src/bicpl-1.4.6/Images/rgb_io_ppm.c:95: undefined reference to `ppm_writeppminit'
>> /usr/local/minc/src/bicpl-1.4.6/Images/rgb_io_ppm.c:98: undefined reference to `ppm_allocrow'
>> /usr/local/minc/src/bicpl-1.4.6/Images/rgb_io_ppm.c:116: undefined reference to `ppm_writeppmrow'
>> /usr/local/minc/lib/libbicpl.a(rgb_io.o): In function `input_rgb_file':
>> /usr/local/minc/src/bicpl-1.4.6/Images/rgb_io_ppm.c:29: undefined reference to `ppm_readppminit'
>> /usr/local/minc/src/bicpl-1.4.6/Images/rgb_io_ppm.c:31: undefined reference to `ppm_allocrow'
>> /usr/local/minc/src/bicpl-1.4.6/Images/rgb_io_ppm.c:44: undefined reference to `ppm_readppmrow'
>> collect2: ld returned 1 exit status
>>
>>
>> Michael
>> ________________________________________
>> From: minc-users-bounces at bic.mni.mcgill.ca [minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Andrew Janke [a.janke at gmail.com]
>> Sent: Thursday, April 07, 2011 3:09 AM
>> To: MINC users mailing list
>> Subject: Re: [MINC-users] build almost everything minc Makefile and git repository for EZminc
>>
>>> Okay, I tried that, but I still get this message:
>>>
>>> <unimportant tmpdir thing>
>>> /usr/local/minc/src/bicpl-1.4.6/Images/rgb_io_ppm.c:98: undefined reference to `ppm_allocrow'
>>> /usr/local/minc/lib/libbicpl.a(rgb_io.o): In function `input_rgb_file':
>>> /usr/local/minc/src/bicpl-1.4.6/Images/rgb_io_ppm.c:31: undefined reference to `ppm_allocrow'
>>> collect2: ld returned 1 exit status
>>
>> ah, ppm_allocrow, did you link bicpl with ppm or netpbm?
>>
>> I am not sure which platform you are compiling this on but on some
>> architectures you have to link with:
>>
>>    -lpgm -lpbm
>>
>>
>> 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
>
>
> --
> Best regards,
>  Vladimir S. FONOV ~ v.s.fonov  <at> ilmarin.info
> _______________________________________________
> 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 atipirne at stanford.edu  Fri May 20 18:11:47 2011
From: atipirne at stanford.edu (Aaryani Tipirneni)
Date: Fri, 20 May 2011 15:11:47 -0700 (PDT)
Subject: [MINC-users] Cerebral hemisphere mask: ICBM minc atlas
Message-ID: <205205399.465897.1305929507757.JavaMail.root@zm04.stanford.edu>

Hi MINC users,

  Could you please tell me if there is a cerebrum mask (i.e., excluding cerebellum and brain stem from the whole brain) that could be downloaded for the ICBM/MNI atlas.

Thanks in advance,
Aaryani

From a.janke at gmail.com  Sat May 21 09:56:01 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Sat, 21 May 2011 23:56:01 +1000
Subject: [MINC-users] Cerebral hemisphere mask: ICBM minc atlas
In-Reply-To: <205205399.465897.1305929507757.JavaMail.root@zm04.stanford.edu>
References: <205205399.465897.1305929507757.JavaMail.root@zm04.stanford.edu>
Message-ID: <BANLkTi=paxz=1XdCYotNSXmEWzkmHQNbrQ@mail.gmail.com>

Hi Aaryani

On Sat, May 21, 2011 at 08:11, Aaryani Tipirneni <atipirne at stanford.edu> wrote:
> ?Could you please tell me if there is a cerebrum mask (i.e., excluding cerebellum and brain stem from the whole brain) that could be downloaded for the ICBM/MNI atlas.

There is not one in the current released MINC packages. There is
however one in a package of Louis Collins' called lobe_segment. I am
not sure if this package will be released or not but you could
certainly email Louis directly and ask for a copy of the package.

Thanks


Andrew

From se at hst.aau.dk  Mon May 23 13:26:59 2011
From: se at hst.aau.dk (Simon Fristed Eskildsen)
Date: Mon, 23 May 2011 13:26:59 -0400
Subject: [MINC-users] Cerebral hemisphere mask: ICBM minc atlas
In-Reply-To: <BANLkTi=paxz=1XdCYotNSXmEWzkmHQNbrQ@mail.gmail.com>
References: <205205399.465897.1305929507757.JavaMail.root@zm04.stanford.edu>
	<BANLkTi=paxz=1XdCYotNSXmEWzkmHQNbrQ@mail.gmail.com>
Message-ID: <BANLkTimvHTfML05qTBEcHeYe1KjWNzFUAg@mail.gmail.com>

Hi Aaryani,

I have a cerebrum mask for the ICBM152. It can be downloaded here:

http://person.hst.aau.dk/se/resources/ICBM152_cerebrum_mask.mnc.gz

It's generated using the cortical extraction method FACE from the
non-linear ICBM template. It should fit with the linear template as
well.
CSF in the larger sulci / fissures are not included in the mask. This
can probably be included by dilation (or closing) operations.

Simon

On Sat, May 21, 2011 at 9:56 AM, Andrew Janke <a.janke at gmail.com> wrote:
> Hi Aaryani
>
> On Sat, May 21, 2011 at 08:11, Aaryani Tipirneni <atipirne at stanford.edu> wrote:
>> ?Could you please tell me if there is a cerebrum mask (i.e., excluding cerebellum and brain stem from the whole brain) that could be downloaded for the ICBM/MNI atlas.
>
> There is not one in the current released MINC packages. There is
> however one in a package of Louis Collins' called lobe_segment. I am
> not sure if this package will be released or not but you could
> certainly email Louis directly and ask for a copy of the package.
>
> Thanks
>
>
> Andrew

From michel.audette at kitware.com  Wed May 25 18:17:40 2011
From: michel.audette at kitware.com (Michel Audette)
Date: Wed, 25 May 2011 18:17:40 -0400
Subject: [MINC-users] how to pad prior to distance computation with mincmorph
Message-ID: <BANLkTikfVsxVVrvbvmMP0e7-7jBwJq8cAA@mail.gmail.com>

Dear fellow Minc users,

I'm trying to use mincmorph to compute a distance transform from a binary
image, and finding that the algorithm also seems to initialize distance at 0
at the boundary of the image. I assume that the answer lies in padding the
volume prior to the distance transform, and I can see that there is an
option for that, but I can't seem to get that part of the computation
working properly. Can anyone show an example of this use?

Best wishes,

Michel

-- 
Michel Audette, Ph.D.
R & D Engineer,
Kitware Inc.,
Chapel Hill, N.C.

From a.janke at gmail.com  Wed May 25 18:47:54 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 26 May 2011 08:47:54 +1000
Subject: [MINC-users] how to pad prior to distance computation with
	mincmorph
In-Reply-To: <BANLkTikfVsxVVrvbvmMP0e7-7jBwJq8cAA@mail.gmail.com>
References: <BANLkTikfVsxVVrvbvmMP0e7-7jBwJq8cAA@mail.gmail.com>
Message-ID: <BANLkTikoO9a075qhiNCFc+D4Gy2+9L8npA@mail.gmail.com>

Hi Michel,

On Thu, May 26, 2011 at 08:17, Michel Audette
<michel.audette at kitware.com> wrote:
> I'm trying to use mincmorph to compute a distance transform from a binary
> image, and finding that the algorithm also seems to initialize distance at 0
> at the boundary of the image. I assume that the answer lies in padding the
> volume prior to the distance transform, and I can see that there is an
> option for that, but I can't seem to get that part of the computation
> working properly. Can anyone show an example of this use?

I am guessing that you will want something like this:

   $ mincmorph -successive 'B[0:100]PF' <in.mnc> <out.mnc>

This will first binarise the image between 0 and 100, then pad it
(using the size of the kernel currently in use) and then do the
distance transformation.


a

From michel.audette at kitware.com  Tue May 31 17:00:07 2011
From: michel.audette at kitware.com (Michel Audette)
Date: Tue, 31 May 2011 17:00:07 -0400
Subject: [MINC-users] how to pad prior to distance computation with
	mincmorph
In-Reply-To: <BANLkTikoO9a075qhiNCFc+D4Gy2+9L8npA@mail.gmail.com>
References: <BANLkTikfVsxVVrvbvmMP0e7-7jBwJq8cAA@mail.gmail.com>
	<BANLkTikoO9a075qhiNCFc+D4Gy2+9L8npA@mail.gmail.com>
Message-ID: <BANLkTikyjqCwrNKChjANpfJNb9hkXte9mw@mail.gmail.com>

Hi Andrew,

sorry this is late. Thanks for your kind reply. I'll give it a try.

Best wishes,

Michel

On Wed, May 25, 2011 at 6:47 PM, Andrew Janke <a.janke at gmail.com> wrote:

> Hi Michel,
>
> On Thu, May 26, 2011 at 08:17, Michel Audette
> <michel.audette at kitware.com> wrote:
> > I'm trying to use mincmorph to compute a distance transform from a binary
> > image, and finding that the algorithm also seems to initialize distance
> at 0
> > at the boundary of the image. I assume that the answer lies in padding
> the
> > volume prior to the distance transform, and I can see that there is an
> > option for that, but I can't seem to get that part of the computation
> > working properly. Can anyone show an example of this use?
>
> I am guessing that you will want something like this:
>
>   $ mincmorph -successive 'B[0:100]PF' <in.mnc> <out.mnc>
>
> This will first binarise the image between 0 and 100, then pad it
> (using the size of the kernel currently in use) and then do the
> distance transformation.
>
>
> a
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



-- 
Michel Audette, Ph.D.
R & D Engineer,
Kitware Inc.,
Chapel Hill, N.C.