From thomas.funck at mail.mcgill.ca  Mon Apr  4 10:24:03 2011
From: thomas.funck at mail.mcgill.ca (Thomas Funck)
Date: Mon, 4 Apr 2011 14:24:03 +0000
Subject: [MINC-users] MINC-users Digest, Vol 68, Issue 24
In-Reply-To: <mailman.5.1301587202.8612.minc-users@bic.mni.mcgill.ca>
References: <mailman.5.1301587202.8612.minc-users@bic.mni.mcgill.ca>
Message-ID: <53F3FD0032C9CC4BA836E8F0FC289065D202@EXMBX2010-2.campus.MCGILL.CA>

Hi, 

I'm having trouble creating a 4 dimensional volume with the function micreate_volume, the function returns -1 whenever I try to use it . I'm basically using the exact same code as is contained in the minc2 tutorials, except that I changed the type from ubyte to double (it doesn't work with either type). The strange thing is that the function works fine for 3 dimensional volumes. I'm sure that the dimensions are set correctly so that isn't the problem. Any ideas what's causing this? 

Many thanks,

Thomas


P.S.
Here are the lines of code in question:

  mihandle_t    minc_volume, new_volume;
  midimhandle_t dimensions[4];
  unsigned int  sizes[4];

  
   miopen_volume(argv[1], MI2_OPEN_READ, &minc_volume);

  miget_volume_dimensions(minc_volume, MI_DIMCLASS_ANY, MI_DIMATTR_ALL, MI_DIMORDER_FILE,  4, dimensions);
  miget_dimension_sizes(dimensions, 4, sizes);
 
  micreate_volume(argv[2], 4, dimensions, MI_TYPE_DOUBLE,MI_CLASS_REAL, NULL, &new_volume)

From MKeaser at umaryland.edu  Mon Apr  4 12:52:41 2011
From: MKeaser at umaryland.edu (Keaser, Michael L)
Date: Mon, 4 Apr 2011 12:52:41 -0400
Subject: [MINC-users] build almost everything minc Makefile and git
 repository for EZminc
In-Reply-To: <AANLkTikeG=aYEP4k4weRZbAtB9r50Wekz7aw5+FHU=D7@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>
Message-ID: <00EF2C3B391AF84C8ED343F4469D4D56055F5BC2CE@UMBEXMBX2.campus.umaryland.edu>

Andrew,

I'm still having trouble installing Display.

When you say "copy and paste the last line of the build (when Display is made) and then run it without the liibtool part", which specific "build" file are you referring to where we can make this edit?

Thanks,

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: Tuesday, March 29, 2011 8:16 AM
To: MINC users mailing list
Subject: Re: [MINC-users] build almost everything minc Makefile and git repository for EZminc

If this is the same "bug" that I have been bitten by it's to do with
libtool and the way bicpl is linked (or not as the case often turns
out to be) with libnetpbm.

If you run make in the Display directory, copy and paste the last line
of the build (when Display is made) and then run it without the
libtool part.  turn

   $ libtool <blah> gcc <blah>

into

   $ gcc <blah>

and in most cases Display will be made.

YMMV but this is what I have seen but haven't got to the bottom of yet.

a

On Tue, Mar 29, 2011 at 09:34, Mishkin Derakhshan <mishkind at gmail.com> wrote:
> Then I tried debugging:
> Inside the source dir of Display-1.5.0
> ./configure --prefix=/usr/local/bic --with-build-path=/usr/local/bic
> --with-minc2 --with-x
> make
_______________________________________________
MINC-users at bic.mni.mcgill.ca
http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From anthonin at bic.mni.mcgill.ca  Mon Apr  4 21:15:03 2011
From: anthonin at bic.mni.mcgill.ca (Anthonin REILHAC)
Date: Mon, 4 Apr 2011 21:15:03 -0400 (EDT)
Subject: [MINC-users] ecattominc seg fault on 64-bit Lucid
In-Reply-To: <AANLkTi=Mojo5BvePmdS_qLMQZ+Uvh5HVm7g9bnbh0gs0@mail.gmail.com>
References: <AANLkTi=Mojo5BvePmdS_qLMQZ+Uvh5HVm7g9bnbh0gs0@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.1104042112190.3313@cassio.bic.mni.mcgill.ca>


I still see this issue once in a while.
I fixed the bug for 64 bits machine some years ago.
But it seems that the correct version is still notincluded in the distros.
to whom should I send the correct version?

Cheers,



Anthonin Reilhac
McConnell Brain Imaging Centre, WB2B
Montreal Neurological Institute
3801 University
Montreal, Quebec, Canada

phone: (514) 398 4965

On Tue, 4 Jan 2011, EJ Nikelski wrote:

> Hi All,
>
>   I've been using ecattominc to convert 7-frame dynamic volumes
> (acquired at the MNI) to minc for some time, without any trouble.
> Today, however, I installed the minc tools on to a relatively fresh
> 64-bit Lucid system, and I'm now getting seg faults (minc-2.1.00). The
> abort occurs consistently while opening the ecat file and appears to
> occur within the "/* Save the offsets */" loop of function
> ecat_read_directory (ecat_file.c). The precise loop number at which
> the seg fault occurs is variable, suggesting that this is related
> either to an uninitialized variable, or some 32-bit versus 64-bit
> issue (the same ecat volume does not cause a seg fault on our 32-bit
> system).
>
>  Any ideas or suggestions?  I'm willing to test any suggested code
> modifications.  I've already done a fair bit of poking around and
> re-compiling, but my knowledge of ecat header internals is lacking.
>
> Thanks,
>
> -jim
>
> -- 
> =================================
> Jim Nikelski, Ph.D.
> Postdoctoral Research Fellow
> Bloomfield Centre for Research in Aging
> Lady Davis Institute for Medical Research
> Sir Mortimer B. Davis - Jewish General Hospital
> McGill University
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From a.janke at gmail.com  Mon Apr  4 21:35:07 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 5 Apr 2011 11:35:07 +1000
Subject: [MINC-users] ecattominc seg fault on 64-bit Lucid
In-Reply-To: <Pine.LNX.4.64.1104042112190.3313@cassio.bic.mni.mcgill.ca>
References: <AANLkTi=Mojo5BvePmdS_qLMQZ+Uvh5HVm7g9bnbh0gs0@mail.gmail.com>
	<Pine.LNX.4.64.1104042112190.3313@cassio.bic.mni.mcgill.ca>
Message-ID: <BANLkTi=aFN62zHQTHk+1z2T0o00jrkTh1g@mail.gmail.com>

> I still see this issue once in a while.
> I fixed the bug for 64 bits machine some years ago.
> But it seems that the correct version is still notincluded in the distros.
> to whom should I send the correct version?

Hrm, well this might be a good time to mention this:

   https://github.com/andrewjanke/minc

MINC is/will be/probably eventually shifting to GIT on NITRC so that
others can more easily contribute. As I trial I have imported the
entire of the MINC CVS history to github. For now it is the primary
source of MINC and I will be syncing changes made there back to the
MINC CVS at the BIC.

So please check the version on github, if it is still wrong then by
all means add yourself as a user on github, send me the name and I
will add you as a developer. We (minc devs) are aiming for a more open
MINC from here on in so hopefully a change to github or NITRC will
lower the bar for others to contribute.

Thanks


-- 
Andrew Janke
(a.janke at gmail.com || http://a.janke.googlepages.com/)
Brisbane->Australia    +61 (402) 700 883

From mishkind at gmail.com  Mon Apr  4 21:44:40 2011
From: mishkind at gmail.com (Mishkin Derakhshan)
Date: Mon, 4 Apr 2011 21:44:40 -0400
Subject: [MINC-users] build almost everything minc Makefile and git
 repository for EZminc
In-Reply-To: <00EF2C3B391AF84C8ED343F4469D4D56055F5BC2CE@UMBEXMBX2.campus.umaryland.edu>
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>
Message-ID: <BANLkTi=4kUd2TvC0w3OGvcBqgva03P0mrQ@mail.gmail.com>

Hi Keaser
if you did something like this for vlad's Makefile:

make Display PREFIX=/usr/local/bic TEMP=$HOME/temp

then try this

cd $HOME/src/Display-1.5.0
./configure --prefix=/usr/local/bic --with-build-path=/usr/local/bic
--with-minc2 --with-x
make

(lots of screen output)

The last line for me is:
/bin/bash ./libtool --tag=CC   --mode=link gcc  -g -O2
-L/usr/local/bic/lib -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  -lbicpl -lvolume_io2
-lminc2 -lhdf5 -lz -lnetcdf -lm -lm   -lbicpl -lvolume_io2 -lminc2
-lhdf5 -lz -lnetcdf -lm -lm

So you would just do:
gcc  -g -O2  -L/usr/local/bic/lib -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  -lbicpl -lvolume_io2
-lminc2 -lhdf5 -lz -lnetcdf -lm -lm   -lbicpl -lvolume_io2 -lminc2
-lhdf5 -lz -lnetcdf -lm -lm

Unfortunately, I still get an error and there is no executable
slice_window/crop.o: In function `crop_and_load_volume':
/home/mishkin/src/Display-1.5.0/slice_window/crop.c:165: warning: the
use of `tmpnam' is dangerous, better use `mkstemp'
/usr/local/bic/lib/libbicpl.a(rgb_io.o): In function `output_rgb_file':
/home/mishkin/src/bicpl-1.4.6/Images/rgb_io_ppm.c:95: undefined
reference to `ppm_writeppminit'
/home/mishkin/src/bicpl-1.4.6/Images/rgb_io_ppm.c:98: undefined
reference to `ppm_allocrow'
/home/mishkin/src/bicpl-1.4.6/Images/rgb_io_ppm.c:116: undefined
reference to `ppm_writeppmrow'
/usr/local/bic/lib/libbicpl.a(rgb_io.o): In function `input_rgb_file':
/home/mishkin/src/bicpl-1.4.6/Images/rgb_io_ppm.c:29: undefined
reference to `ppm_readppminit'
/home/mishkin/src/bicpl-1.4.6/Images/rgb_io_ppm.c:31: undefined
reference to `ppm_allocrow'
/home/mishkin/src/bicpl-1.4.6/Images/rgb_io_ppm.c:44: undefined
reference to `ppm_readppmrow'
collect2: ld returned 1 exit status

Maybe you will have better luck, or maybe the people much smarter than
me will be able to help you.

mishkin

On Mon, Apr 4, 2011 at 12:52 PM, Keaser, Michael L
<MKeaser at umaryland.edu> wrote:
> Andrew,
>
> I'm still having trouble installing Display.
>
> When you say "copy and paste the last line of the build (when Display is made) and then run it without the liibtool part", which specific "build" file are you referring to where we can make this edit?
>
> Thanks,
>
> 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: Tuesday, March 29, 2011 8:16 AM
> To: MINC users mailing list
> Subject: Re: [MINC-users] build almost everything minc Makefile and git repository for EZminc
>
> If this is the same "bug" that I have been bitten by it's to do with
> libtool and the way bicpl is linked (or not as the case often turns
> out to be) with libnetpbm.
>
> If you run make in the Display directory, copy and paste the last line
> of the build (when Display is made) and then run it without the
> libtool part. ?turn
>
> ? $ libtool <blah> gcc <blah>
>
> into
>
> ? $ gcc <blah>
>
> and in most cases Display will be made.
>
> YMMV but this is what I have seen but haven't got to the bottom of yet.
>
> a
>
> On Tue, Mar 29, 2011 at 09:34, Mishkin Derakhshan <mishkind at gmail.com> wrote:
>> Then I tried debugging:
>> Inside the source dir of Display-1.5.0
>> ./configure --prefix=/usr/local/bic --with-build-path=/usr/local/bic
>> --with-minc2 --with-x
>> make
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From a.janke at gmail.com  Mon Apr  4 21:51:17 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 5 Apr 2011 11:51:17 +1000
Subject: [MINC-users] build almost everything minc Makefile and git
 repository for EZminc
In-Reply-To: <BANLkTi=4kUd2TvC0w3OGvcBqgva03P0mrQ@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>
Message-ID: <BANLkTimyZV9Gtc5GOaPNq8RAz61Mt8fc5w@mail.gmail.com>

> <chomp correct things>

On Tue, Apr 5, 2011 at 11:44, Mishkin Derakhshan <mishkind at gmail.com> wrote:
> Unfortunately, I still get an error and there is no executable
> slice_window/crop.o: In function `crop_and_load_volume':
> /home/mishkin/src/Display-1.5.0/slice_window/crop.c:165: warning: the
> use of `tmpnam' is dangerous, better use `mkstemp'
> /usr/local/bic/lib/libbicpl.a(rgb_io.o): In function `output_rgb_file':
> /home/mishkin/src/bicpl-1.4.6/Images/rgb_io_ppm.c:95: undefined
> reference to `ppm_writeppminit'
> /home/mishkin/src/bicpl-1.4.6/Images/rgb_io_ppm.c:98: undefined
> reference to `ppm_allocrow'
> /home/mishkin/src/bicpl-1.4.6/Images/rgb_io_ppm.c:116: undefined
> reference to `ppm_writeppmrow'
> /usr/local/bic/lib/libbicpl.a(rgb_io.o): In function `input_rgb_file':
> /home/mishkin/src/bicpl-1.4.6/Images/rgb_io_ppm.c:29: undefined
> reference to `ppm_readppminit'
> /home/mishkin/src/bicpl-1.4.6/Images/rgb_io_ppm.c:31: undefined
> reference to `ppm_allocrow'
> /home/mishkin/src/bicpl-1.4.6/Images/rgb_io_ppm.c:44: undefined
> reference to `ppm_readppmrow'
> collect2: ld returned 1 exit status
>
> Maybe you will have better luck, or maybe the people much smarter than
> me will be able to help you.

add -lppm to the link line (after -lm is a good spot).

This is a libtool issue, when you link with -lbicpl it should then
also include -lppm but it doesn't for some reason in all cases.


a

From MKeaser at umaryland.edu  Tue Apr  5 10:56:48 2011
From: MKeaser at umaryland.edu (Keaser, Michael L)
Date: Tue, 5 Apr 2011 10:56:48 -0400
Subject: [MINC-users] build almost everything minc Makefile and git
 repository for EZminc
In-Reply-To: <BANLkTimyZV9Gtc5GOaPNq8RAz61Mt8fc5w@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>
Message-ID: <00EF2C3B391AF84C8ED343F4469D4D56055F5BC2D2@UMBEXMBX2.campus.umaryland.edu>

Andrew,

Thank you Mishkin for your suggestion. It got me pointed in the right direction. I receive the same error message as you do now.

Andrew, where is the "link line" you are referring to? There are few number of lm's. I tried puttng at the very end:

gcc  -g -O2  -L/usr/local/minc/lib -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  -lbicpl -lvolume_io2 -lminc2 -lhdf5 -lz -lnetcdf -lm -lm   -lbicpl -lvolume_io2 -lminc2 -lhdf5 -lz -lnetcdf -lm -lm -lppm

And this is the error message I received

slice_window/crop.o: In function `crop_and_load_volume':
/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: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 statu


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: Monday, April 04, 2011 9:51 PM
To: MINC users mailing list
Subject: Re: [MINC-users] build almost everything minc Makefile and git repository for EZminc

> <chomp correct things>

On Tue, Apr 5, 2011 at 11:44, Mishkin Derakhshan <mishkind at gmail.com> wrote:
> Unfortunately, I still get an error and there is no executable
> slice_window/crop.o: In function `crop_and_load_volume':
> /home/mishkin/src/Display-1.5.0/slice_window/crop.c:165: warning: the
> use of `tmpnam' is dangerous, better use `mkstemp'
> /usr/local/bic/lib/libbicpl.a(rgb_io.o): In function `output_rgb_file':
> /home/mishkin/src/bicpl-1.4.6/Images/rgb_io_ppm.c:95: undefined
> reference to `ppm_writeppminit'
> /home/mishkin/src/bicpl-1.4.6/Images/rgb_io_ppm.c:98: undefined
> reference to `ppm_allocrow'
> /home/mishkin/src/bicpl-1.4.6/Images/rgb_io_ppm.c:116: undefined
> reference to `ppm_writeppmrow'
> /usr/local/bic/lib/libbicpl.a(rgb_io.o): In function `input_rgb_file':
> /home/mishkin/src/bicpl-1.4.6/Images/rgb_io_ppm.c:29: undefined
> reference to `ppm_readppminit'
> /home/mishkin/src/bicpl-1.4.6/Images/rgb_io_ppm.c:31: undefined
> reference to `ppm_allocrow'
> /home/mishkin/src/bicpl-1.4.6/Images/rgb_io_ppm.c:44: undefined
> reference to `ppm_readppmrow'
> collect2: ld returned 1 exit status
>
> Maybe you will have better luck, or maybe the people much smarter than
> me will be able to help you.

add -lppm to the link line (after -lm is a good spot).

This is a libtool issue, when you link with -lbicpl it should then
also include -lppm but it doesn't for some reason in all cases.


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

From a.janke at gmail.com  Tue Apr  5 11:09:33 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 6 Apr 2011 01:09:33 +1000
Subject: [MINC-users] build almost everything minc Makefile and git
 repository for EZminc
In-Reply-To: <00EF2C3B391AF84C8ED343F4469D4D56055F5BC2D2@UMBEXMBX2.campus.umaryland.edu>
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>
Message-ID: <BANLkTinY-+2bHvHFTz0z3S6ZkzpkgN4qnQ@mail.gmail.com>

> Thank you Mishkin for your suggestion. It got me pointed in the right direction. I receive the same error message as you do now.
>
> Andrew, where is the "link line" you are referring to? There are few number of lm's. I tried puttng at the very end:

Ah, it will have to go before -lbicpl


a

From MKeaser at umaryland.edu  Tue Apr  5 11:22:59 2011
From: MKeaser at umaryland.edu (Keaser, Michael L)
Date: Tue, 5 Apr 2011 11:22:59 -0400
Subject: [MINC-users] build almost everything minc Makefile and git
 repository for EZminc
In-Reply-To: <BANLkTinY-+2bHvHFTz0z3S6ZkzpkgN4qnQ@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>
Message-ID: <00EF2C3B391AF84C8ED343F4469D4D56055F5BC2D3@UMBEXMBX2.campus.umaryland.edu>

Andrew,

Okay, I tried that, but I still get 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: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


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: Tuesday, April 05, 2011 11:09 AM
To: MINC users mailing list
Subject: Re: [MINC-users] build almost everything minc Makefile and git repository for EZminc

> Thank you Mishkin for your suggestion. It got me pointed in the right direction. I receive the same error message as you do now.
>
> Andrew, where is the "link line" you are referring to? There are few number of lm's. I tried puttng at the very end:

Ah, it will have to go before -lbicpl


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

From baghdadi at phenogenomics.ca  Wed Apr  6 09:49:10 2011
From: baghdadi at phenogenomics.ca (Leila Baghdadi)
Date: Wed, 6 Apr 2011 09:49:10 -0400
Subject: [MINC-users] FW:  MINC-users Digest, Vol 68, Issue 24
Message-ID: <14191403.116921302097750589.JavaMail.root@mail2.phenogenomics.ca>

Hello,

I just took a quick look at your test code and it seems to
 me that you are not creating a 4 dimensional volume but trying to load 
an existing one. either way, there should not be any trouble with the 
code!

For creating a 4D volume, check minc2.0(any version will have this)/libsrc2/test/create-test-images.c

I
 have used 4D volumes in the past and do not recall any problems, if you
 are trying to load a 4D volume and have difficulty, please let me know 
the location of it so I can check it out.

Leila
p.s the test 
directory "libsrc2/test" of minc2 has a number of very good test code 
snippet, I think you will find them very useful 

From a.janke at gmail.com  Thu Apr  7 03:09:59 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 7 Apr 2011 17:09:59 +1000
Subject: [MINC-users] build almost everything minc Makefile and git
 repository for EZminc
In-Reply-To: <00EF2C3B391AF84C8ED343F4469D4D56055F5BC2D3@UMBEXMBX2.campus.umaryland.edu>
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>
Message-ID: <BANLkTikH2G3KgoNL_nPaMqWD1bAOVi0jyA@mail.gmail.com>

> 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

From MKeaser at umaryland.edu  Thu Apr  7 10:16:47 2011
From: MKeaser at umaryland.edu (Keaser, Michael L)
Date: Thu, 7 Apr 2011 10:16:47 -0400
Subject: [MINC-users] build almost everything minc Makefile and git
 repository for EZminc
In-Reply-To: <BANLkTikH2G3KgoNL_nPaMqWD1bAOVi0jyA@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>
Message-ID: <00EF2C3B391AF84C8ED343F4469D4D56055F5BC2D8@UMBEXMBX2.campus.umaryland.edu>

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

From vladimir.fonov at gmail.com  Thu Apr  7 11:19:12 2011
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Thu, 07 Apr 2011 11:19:12 -0400
Subject: [MINC-users] build almost everything minc Makefile and git
 repository for EZminc
In-Reply-To: <00EF2C3B391AF84C8ED343F4469D4D56055F5BC2D8@UMBEXMBX2.campus.umaryland.edu>
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>
Message-ID: <4D9DD5F0.3020002@gmail.com>

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

From MKeaser at umaryland.edu  Thu Apr  7 11:49:00 2011
From: MKeaser at umaryland.edu (Keaser, Michael L)
Date: Thu, 7 Apr 2011 11:49:00 -0400
Subject: [MINC-users] build almost everything minc Makefile and git
 repository for EZminc
In-Reply-To: <4D9DD5F0.3020002@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>
Message-ID: <00EF2C3B391AF84C8ED343F4469D4D56055F5BC2DC@UMBEXMBX2.campus.umaryland.edu>

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

From vladimir.fonov at gmail.com  Thu Apr  7 11:59:43 2011
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Thu, 7 Apr 2011 11:59:43 -0400
Subject: [MINC-users] build almost everything minc Makefile and git
 repository for EZminc
In-Reply-To: <00EF2C3B391AF84C8ED343F4469D4D56055F5BC2DC@UMBEXMBX2.campus.umaryland.edu>
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>
Message-ID: <BANLkTikmohrVn0EKbvzZ535hOwekRDX8Ow@mail.gmail.com>

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

From lrisa87 at uw.edu  Thu Apr  7 14:05:19 2011
From: lrisa87 at uw.edu (Lisa F. Akiyama)
Date: Thu, 7 Apr 2011 11:05:19 -0700
Subject: [MINC-users] best_nonlin_reg.pl ?
In-Reply-To: <AANLkTimw3cqJs_+zjngwj-JqCxpTVRdHFz+ejbeTktZ0@mail.gmail.com>
References: <AANLkTinqOrw0G9dC-o4obCD62=eyzyJL=4oj+9zvnpsc@mail.gmail.com>
	<201102250344.p1P3i5tq002657@cassio.bic.mni.mcgill.ca>
	<AANLkTinRWRtwxpXCm3N=BiuCTF2cpifgX2Ta_shkGAvX@mail.gmail.com>
	<AANLkTinxoxfGz9T2eYk2RnMHgeHWbhqreJkxSzWAKdpX@mail.gmail.com>
	<AANLkTimYRbWUbZ10-jCrg-SOr8x9tJ17kvviv++Dc6rj@mail.gmail.com>
	<AANLkTim9krZyo5W=9oDhgGmLhrt5xhYGfbg27RALLQ5K@mail.gmail.com>
	<AANLkTin8V9TVxxd5kx2VPEeE5CoCe-y8kgzTNC780tbK@mail.gmail.com>
	<4D6D8AD8.5000707@gmail.com>
	<AANLkTi=qP=89E-KJo=Qy=bNDg5keOMNZdgNjcskqRdtF@mail.gmail.com>
	<AANLkTika+hX+3On4ro+ExMZ=f7hpzyTCXNdB3z+aMBQ1@mail.gmail.com>
	<AANLkTim1OH+Exj7fXMrtn7VR-sKWPZ0kWN49c-qUzPii@mail.gmail.com>
	<AANLkTi=zuYHxSUMwmUcTaLhU7mtR7mLMs-TwwbjMtHtL@mail.gmail.com>
	<AANLkTi=PKHN51grinEVpF=HeRgjHJC+EbA+27WxLE-9N@mail.gmail.com>
	<AANLkTimu3XFmgfofKZE9xZDMgHmOR1SVyKatgwSOvZcS@mail.gmail.com>
	<AANLkTimw3cqJs_+zjngwj-JqCxpTVRdHFz+ejbeTktZ0@mail.gmail.com>
Message-ID: <BANLkTikiBW_JAL+V7ywzpRGV8oxWtuvhhw@mail.gmail.com>

Hello,

I am using volgenmodel to create a model. I have installed Octave, but I am
still getting the following error and can't figure out what is the issue:

...bestlinreg.xfm genmodel-work/07/avgxfm.xfm
> Processing:........................miicv_attach: MINC package entry point
> ncvarid: ncid -1: NetCDF: Not a valid ID

Died at /usr/local/bic/bin/xfmavg line 310.
> Died at /usr/local/bic/bin/volgenmodel line 656.


I've tried using volgenmodel for two different fit.conf settings and get the
same error at
about the same time point in the course of running this script.
This error appears some point after the "07" folder and some, if not all, of
their contents are created in the working directory.

 What could be some possible causes? Am I missing some other required
script?

Thanks.


Best,
Lisa
 ______________________________




On Thu, Mar 3, 2011 at 11:08 AM, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:

> Hi Andrew,
>
> I did not have Octave installed.
> Right now I am re-running volgenmodel after I installed Octave
> and so far it seems like it is chugging along without any errors at all.
>
> Thanks for all the tips and suggestions!
>
>
> Best,
> Lisa
>
>
>
>
>
> On Thu, Mar 3, 2011 at 5:15 AM, Andrew Janke <a.janke at gmail.com> wrote:
>
>> Hi Lisa,
>>
>> >> Died at /usr/local/bic/bin/xfmavg line 310.
>> >> Died at /usr/local/bic/bin/volgenmodel line 656.
>> >
>> > The output file that I specified the name of is no where to be found in
>> the
>> > workdir or the dir where I have stored my input files.
>>
>> I think the output is a big misleading in that I think the problem is
>> in the transform averaging not in the fitting. Do you have octave
>> installed?  xfmavg uses this.
>>
>> perhaps if you add a -verbose argument things might become a bit more
>> clear?  volgenmodel is designed such that you can just re-run whatever
>> you did last and it will pick up from where it left off.
>>
>> There is even a copy of the original command you used in the
>> genmodel-work directory.
>>
>>
>> a
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>
>

From a.janke at gmail.com  Thu Apr  7 20:09:44 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Fri, 8 Apr 2011 10:09:44 +1000
Subject: [MINC-users] best_nonlin_reg.pl ?
In-Reply-To: <BANLkTikiBW_JAL+V7ywzpRGV8oxWtuvhhw@mail.gmail.com>
References: <AANLkTinqOrw0G9dC-o4obCD62=eyzyJL=4oj+9zvnpsc@mail.gmail.com>
	<201102250344.p1P3i5tq002657@cassio.bic.mni.mcgill.ca>
	<AANLkTinRWRtwxpXCm3N=BiuCTF2cpifgX2Ta_shkGAvX@mail.gmail.com>
	<AANLkTinxoxfGz9T2eYk2RnMHgeHWbhqreJkxSzWAKdpX@mail.gmail.com>
	<AANLkTimYRbWUbZ10-jCrg-SOr8x9tJ17kvviv++Dc6rj@mail.gmail.com>
	<AANLkTim9krZyo5W=9oDhgGmLhrt5xhYGfbg27RALLQ5K@mail.gmail.com>
	<AANLkTin8V9TVxxd5kx2VPEeE5CoCe-y8kgzTNC780tbK@mail.gmail.com>
	<4D6D8AD8.5000707@gmail.com>
	<AANLkTi=qP=89E-KJo=Qy=bNDg5keOMNZdgNjcskqRdtF@mail.gmail.com>
	<AANLkTika+hX+3On4ro+ExMZ=f7hpzyTCXNdB3z+aMBQ1@mail.gmail.com>
	<AANLkTim1OH+Exj7fXMrtn7VR-sKWPZ0kWN49c-qUzPii@mail.gmail.com>
	<AANLkTi=zuYHxSUMwmUcTaLhU7mtR7mLMs-TwwbjMtHtL@mail.gmail.com>
	<AANLkTi=PKHN51grinEVpF=HeRgjHJC+EbA+27WxLE-9N@mail.gmail.com>
	<AANLkTimu3XFmgfofKZE9xZDMgHmOR1SVyKatgwSOvZcS@mail.gmail.com>
	<AANLkTimw3cqJs_+zjngwj-JqCxpTVRdHFz+ejbeTktZ0@mail.gmail.com>
	<BANLkTikiBW_JAL+V7ywzpRGV8oxWtuvhhw@mail.gmail.com>
Message-ID: <BANLkTinBcOW9JgC0i_fbSbP8Q5yizp-q3w@mail.gmail.com>

Hi Lisa,

> ...bestlinreg.xfm genmodel-work/07/avgxfm.xfm
>> Processing:........................miicv_attach: MINC package entry point
>> ncvarid: ncid -1: NetCDF: Not a valid ID

> I've tried using volgenmodel for two different fit.conf settings and get the
> same error at
> about the same time point in the course of running this script.
> This error appears some point after the "07" folder and some, if not all, of
> their contents are created in the working directory.
>
> ?What could be some possible causes? Am I missing some other required
> script?

I have tried to make volgenmodel as resistant to steps failing as I
can but it would seem that there is always one more thing that can go
wrong....  My guess is that you have an incomplete xfm file in the 07
step folder and this is causing xfmavg to fail.

You can usually hunt down the culprit by going into this folder and
running minccomplete on all of the .mnc and .xfm files in there.

ie:

   $ ls *.mnc *.xfm | xargs -I {} minccomplete -verbose {}

If any of the files return a -1 instead of 0 something went amiss. The
best approach at this stage is to just remove this file and re-run
volgenmodel at which point it should pick up where it left off.


a

From lrisa87 at uw.edu  Fri Apr  8 17:27:41 2011
From: lrisa87 at uw.edu (Lisa F. Akiyama)
Date: Fri, 8 Apr 2011 14:27:41 -0700
Subject: [MINC-users] best_nonlin_reg.pl ?
In-Reply-To: <BANLkTinBcOW9JgC0i_fbSbP8Q5yizp-q3w@mail.gmail.com>
References: <AANLkTinqOrw0G9dC-o4obCD62=eyzyJL=4oj+9zvnpsc@mail.gmail.com>
	<201102250344.p1P3i5tq002657@cassio.bic.mni.mcgill.ca>
	<AANLkTinRWRtwxpXCm3N=BiuCTF2cpifgX2Ta_shkGAvX@mail.gmail.com>
	<AANLkTinxoxfGz9T2eYk2RnMHgeHWbhqreJkxSzWAKdpX@mail.gmail.com>
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Message-ID: <BANLkTiksDTPm0d5J7Lh5X60cPX5ePx8EFQ@mail.gmail.com>

Hi Andrew,

Thanks for your reply.

I checked both runs of volgenmodel I was performing on the same set of data
but with different configurations - one stopped at creation of working
directory folder 03, the other stopping at folder 07.
In both cases, I also checked the contents of all the folders that were
created prior to 03 and 07, respectively, too, using the minccomplete
command.
However, in all cases, I got only got "0"'s, no "-1"'s. (Please see the
attached text file for a copy of the results I got when running minccomplete
in the 03 folder)
I've removed the 03/07 folder and re-ran volgenmodel, but I still get the
same error...
When I run volgenmodel with the same configurations but with a different set
of subjects, it runs fine...It is puzzling...


Best,
Lisa
 ______________________________
Lisa F. Akiyama
Research Study Assistant
Institute for Learning & Brain Sciences (I-LABS)
University of Washington
Portage Bay Building, BOX 357988
Seattle, WA 98195-7988  U.S.A.
E-mail: lrisa87 at uw.edu

P Please consider the environment before printing this e-mail.



On Thu, Apr 7, 2011 at 5:09 PM, Andrew Janke <a.janke at gmail.com> wrote:

> Hi Lisa,
>
> > ...bestlinreg.xfm genmodel-work/07/avgxfm.xfm
> >> Processing:........................miicv_attach: MINC package entry
> point
> >> ncvarid: ncid -1: NetCDF: Not a valid ID
>
> > I've tried using volgenmodel for two different fit.conf settings and get
> the
> > same error at
> > about the same time point in the course of running this script.
> > This error appears some point after the "07" folder and some, if not all,
> of
> > their contents are created in the working directory.
> >
> >  What could be some possible causes? Am I missing some other required
> > script?
>
> I have tried to make volgenmodel as resistant to steps failing as I
> can but it would seem that there is always one more thing that can go
> wrong....  My guess is that you have an incomplete xfm file in the 07
> step folder and this is causing xfmavg to fail.
>
> You can usually hunt down the culprit by going into this folder and
> running minccomplete on all of the .mnc and .xfm files in there.
>
> ie:
>
>   $ ls *.mnc *.xfm | xargs -I {} minccomplete -verbose {}
>
> If any of the files return a -1 instead of 0 something went amiss. The
> best approach at this stage is to just remove this file and re-run
> volgenmodel at which point it should pick up where it left off.
>
>
> a
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
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Checking a XFM file (init-0018-16549_001_MNI152maskedout_RAS_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0019-16570_001_MNI152maskedout_RAS_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0019-16570_001_MNI152maskedout_RAS_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0020-16591_001_MNI152maskedout_RAS_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0020-16591_001_MNI152maskedout_RAS_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0021-16596_001_MNI152maskedout_RAS_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0021-16596_001_MNI152maskedout_RAS_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0022-16605_001_MNI152maskedout_RAS_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0022-16605_001_MNI152maskedout_RAS_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0023-16615_001_MNI152maskedout_RAS_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0023-16615_001_MNI152maskedout_RAS_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0024-16647_001_MNI152maskedout_RAS_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0024-16647_001_MNI152maskedout_RAS_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0025-16702_001_MNI152maskedout_RAS_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0025-16702_001_MNI152maskedout_RAS_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0026-16706_001_MNI152maskedout_RAS_nu_mincnorm_bestlinreg_nihpd_new_grid_0.mnc)
0
Checking a XFM file (init-0026-16706_001_MNI152maskedout_RAS_nu_mincnorm_bestlinreg_nihpd_new.xfm)
0
Checking a MINC file (init-0027-16734_001_MNI152maskedout_RAS_nu_mincnorm_bestlinreg_nihpd_new_grid_0.mnc)
0
Checking a XFM file (init-0027-16734_001_MNI152maskedout_RAS_nu_mincnorm_bestlinreg_nihpd_new.xfm)
0
Checking a MINC file (init-0028-SEA0092_6mo_May2009_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0028-SEA0092_6mo_May2009_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0029-SEA0094_6mo_May2009_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0029-SEA0094_6mo_May2009_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0030-SEA0102_6mo_Sep2009_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0030-SEA0102_6mo_Sep2009_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0031-SEA0111_6mo_Dec2009_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0031-SEA0111_6mo_Dec2009_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0032-SEA0112_6mo_Dec2009_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0032-SEA0112_6mo_Dec2009_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0033-SEA0120_6mo_Mar2010_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0033-SEA0120_6mo_Mar2010_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0034-SEA0124_6mo_Mar2010_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0034-SEA0124_6mo_Mar2010_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0035-SEA0135_6mo_June2010_t1mpr_flipped_MNI152maskedout-mipav_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0035-SEA0135_6mo_June2010_t1mpr_flipped_MNI152maskedout-mipav_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0036-SEA0136_6mo_May2010_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0036-SEA0136_6mo_May2010_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0037-SEA0141_6mo_July2010_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0037-SEA0141_6mo_July2010_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0038-SEA0152_6mo_Dec2010_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0038-SEA0152_6mo_Dec2010_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0039-SEA0153_7mo_Dec2010_t1mpr_flipped_MNI152maskedout-mipav_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0039-SEA0153_7mo_Dec2010_t1mpr_flipped_MNI152maskedout-mipav_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0040-SEA0154_6mo_Dec2010_t1mpr_flipped_MNI152maskedout-mipav_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0040-SEA0154_6mo_Dec2010_t1mpr_flipped_MNI152maskedout-mipav_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0041-SEA0157_6mo_Jan2011_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0041-SEA0157_6mo_Jan2011_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0
Checking a MINC file (init-0042-SEA0158_6mo_Jan2011_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg_grid_0.mnc)
0
Checking a XFM file (init-0042-SEA0158_6mo_Jan2011_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg.xfm)
0

From lrisa87 at uw.edu  Fri Apr  8 19:28:40 2011
From: lrisa87 at uw.edu (Lisa F. Akiyama)
Date: Fri, 8 Apr 2011 16:28:40 -0700
Subject: [MINC-users] best_nonlin_reg.pl ?
In-Reply-To: <BANLkTiksDTPm0d5J7Lh5X60cPX5ePx8EFQ@mail.gmail.com>
References: <AANLkTinqOrw0G9dC-o4obCD62=eyzyJL=4oj+9zvnpsc@mail.gmail.com>
	<201102250344.p1P3i5tq002657@cassio.bic.mni.mcgill.ca>
	<AANLkTinRWRtwxpXCm3N=BiuCTF2cpifgX2Ta_shkGAvX@mail.gmail.com>
	<AANLkTinxoxfGz9T2eYk2RnMHgeHWbhqreJkxSzWAKdpX@mail.gmail.com>
	<AANLkTimYRbWUbZ10-jCrg-SOr8x9tJ17kvviv++Dc6rj@mail.gmail.com>
	<AANLkTim9krZyo5W=9oDhgGmLhrt5xhYGfbg27RALLQ5K@mail.gmail.com>
	<AANLkTin8V9TVxxd5kx2VPEeE5CoCe-y8kgzTNC780tbK@mail.gmail.com>
	<4D6D8AD8.5000707@gmail.com>
	<AANLkTi=qP=89E-KJo=Qy=bNDg5keOMNZdgNjcskqRdtF@mail.gmail.com>
	<AANLkTika+hX+3On4ro+ExMZ=f7hpzyTCXNdB3z+aMBQ1@mail.gmail.com>
	<AANLkTim1OH+Exj7fXMrtn7VR-sKWPZ0kWN49c-qUzPii@mail.gmail.com>
	<AANLkTi=zuYHxSUMwmUcTaLhU7mtR7mLMs-TwwbjMtHtL@mail.gmail.com>
	<AANLkTi=PKHN51grinEVpF=HeRgjHJC+EbA+27WxLE-9N@mail.gmail.com>
	<AANLkTimu3XFmgfofKZE9xZDMgHmOR1SVyKatgwSOvZcS@mail.gmail.com>
	<AANLkTimw3cqJs_+zjngwj-JqCxpTVRdHFz+ejbeTktZ0@mail.gmail.com>
	<BANLkTikiBW_JAL+V7ywzpRGV8oxWtuvhhw@mail.gmail.com>
	<BANLkTinBcOW9JgC0i_fbSbP8Q5yizp-q3w@mail.gmail.com>
	<BANLkTiksDTPm0d5J7Lh5X60cPX5ePx8EFQ@mail.gmail.com>
Message-ID: <BANLkTikioG8gAa4py-1md+-NrvZS5EPx6g@mail.gmail.com>

Another question on making average models....

I've been creating several preliminary models using different configurations
and methods.
The MNI average brain models for both adults and pediatrics are all straight
in every direction.
However, I look at my resulting models, some of them are a tad tilted in one
or more directions. Going back and checking closely the individuals' scans
that were coregistered (linear 9 parameter registration) to a standard
template,
I find that a few of the coregistered images are slightly tilted. I suspect
that this is why the resulting average model is slightly tilted as well.
Is this a common issue faced when coregistering each individual to a
standard template and creating a model? If so, what are some of the common
ways of fixing them so that the resulting average model will be straight in
every direction and still keeping
the proper MNI space?

Thank you.


Best,
Lisa

On Fri, Apr 8, 2011 at 2:27 PM, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:

> Hi Andrew,
>
> Thanks for your reply.
>
> I checked both runs of volgenmodel I was performing on the same set of data
> but with different configurations - one stopped at creation of working
> directory folder 03, the other stopping at folder 07.
> In both cases, I also checked the contents of all the folders that were
> created prior to 03 and 07, respectively, too, using the minccomplete
> command.
> However, in all cases, I got only got "0"'s, no "-1"'s. (Please see the
> attached text file for a copy of the results I got when running minccomplete
> in the 03 folder)
> I've removed the 03/07 folder and re-ran volgenmodel, but I still get the
> same error...
> When I run volgenmodel with the same configurations but with a different
> set of subjects, it runs fine...It is puzzling...
>
>
> Best,
> Lisa
>  ______________________________
> Lisa F. Akiyama
> Research Study Assistant
> Institute for Learning & Brain Sciences (I-LABS)
> University of Washington
> Portage Bay Building, BOX 357988
> Seattle, WA 98195-7988  U.S.A.
> E-mail: lrisa87 at uw.edu
>
> P Please consider the environment before printing this e-mail.
>
>
>
> On Thu, Apr 7, 2011 at 5:09 PM, Andrew Janke <a.janke at gmail.com> wrote:
>
>> Hi Lisa,
>>
>> > ...bestlinreg.xfm genmodel-work/07/avgxfm.xfm
>> >> Processing:........................miicv_attach: MINC package entry
>> point
>> >> ncvarid: ncid -1: NetCDF: Not a valid ID
>>
>> > I've tried using volgenmodel for two different fit.conf settings and get
>> the
>> > same error at
>> > about the same time point in the course of running this script.
>> > This error appears some point after the "07" folder and some, if not
>> all, of
>> > their contents are created in the working directory.
>> >
>> >  What could be some possible causes? Am I missing some other required
>> > script?
>>
>> I have tried to make volgenmodel as resistant to steps failing as I
>> can but it would seem that there is always one more thing that can go
>> wrong....  My guess is that you have an incomplete xfm file in the 07
>> step folder and this is causing xfmavg to fail.
>>
>> You can usually hunt down the culprit by going into this folder and
>> running minccomplete on all of the .mnc and .xfm files in there.
>>
>> ie:
>>
>>   $ ls *.mnc *.xfm | xargs -I {} minccomplete -verbose {}
>>
>> If any of the files return a -1 instead of 0 something went amiss. The
>> best approach at this stage is to just remove this file and re-run
>> volgenmodel at which point it should pick up where it left off.
>>
>>
>> a
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>
>

From a.janke at gmail.com  Sun Apr 10 22:44:35 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Mon, 11 Apr 2011 12:44:35 +1000
Subject: [MINC-users] best_nonlin_reg.pl ?
In-Reply-To: <BANLkTikioG8gAa4py-1md+-NrvZS5EPx6g@mail.gmail.com>
References: <AANLkTinqOrw0G9dC-o4obCD62=eyzyJL=4oj+9zvnpsc@mail.gmail.com>
	<201102250344.p1P3i5tq002657@cassio.bic.mni.mcgill.ca>
	<AANLkTinRWRtwxpXCm3N=BiuCTF2cpifgX2Ta_shkGAvX@mail.gmail.com>
	<AANLkTinxoxfGz9T2eYk2RnMHgeHWbhqreJkxSzWAKdpX@mail.gmail.com>
	<AANLkTimYRbWUbZ10-jCrg-SOr8x9tJ17kvviv++Dc6rj@mail.gmail.com>
	<AANLkTim9krZyo5W=9oDhgGmLhrt5xhYGfbg27RALLQ5K@mail.gmail.com>
	<AANLkTin8V9TVxxd5kx2VPEeE5CoCe-y8kgzTNC780tbK@mail.gmail.com>
	<4D6D8AD8.5000707@gmail.com>
	<AANLkTi=qP=89E-KJo=Qy=bNDg5keOMNZdgNjcskqRdtF@mail.gmail.com>
	<AANLkTika+hX+3On4ro+ExMZ=f7hpzyTCXNdB3z+aMBQ1@mail.gmail.com>
	<AANLkTim1OH+Exj7fXMrtn7VR-sKWPZ0kWN49c-qUzPii@mail.gmail.com>
	<AANLkTi=zuYHxSUMwmUcTaLhU7mtR7mLMs-TwwbjMtHtL@mail.gmail.com>
	<AANLkTi=PKHN51grinEVpF=HeRgjHJC+EbA+27WxLE-9N@mail.gmail.com>
	<AANLkTimu3XFmgfofKZE9xZDMgHmOR1SVyKatgwSOvZcS@mail.gmail.com>
	<AANLkTimw3cqJs_+zjngwj-JqCxpTVRdHFz+ejbeTktZ0@mail.gmail.com>
	<BANLkTikiBW_JAL+V7ywzpRGV8oxWtuvhhw@mail.gmail.com>
	<BANLkTinBcOW9JgC0i_fbSbP8Q5yizp-q3w@mail.gmail.com>
	<BANLkTiksDTPm0d5J7Lh5X60cPX5ePx8EFQ@mail.gmail.com>
	<BANLkTikioG8gAa4py-1md+-NrvZS5EPx6g@mail.gmail.com>
Message-ID: <BANLkTin7pqCV1trAB9mu6XUN9B_oy7q4zw@mail.gmail.com>

On Sat, Apr 9, 2011 at 09:28, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:
> Another question on making average models....
>
> I've been creating several preliminary models using different configurations
> and methods.
> The MNI average brain models for both adults and pediatrics are all straight
> in every direction.
> However, I look at my resulting models, some of them are a tad tilted in one
> or more directions. Going back and checking closely the individuals' scans
> that were coregistered (linear 9 parameter registration) to a standard
> template,

This depends on whether you making a symmetric or non-symmetric
(default) model. If non-symmetric the resulting image will be in the
average space of all your input images meaning there is a left/Right
rotation bias when your subjects are being scanned.

If you make a symmetric model (add -symmetric to volgenmodel) then
this should not happen.

> Is this a common issue faced when coregistering each individual to a
> standard template and creating a model?

Yes, you are not alone!

> If so, what are some of the common
> ways of fixing them so that the resulting average model will be straight in
> every direction and still keeping
> the proper MNI space?

I have a quick and dirty tool called volalign that does a registration
of an image to itself and then takes 1/2 the resulting translation and
rotation results and applies it. It won't be perfect as you really
should iterate this sort of approach but with one run it will make
things a whole lot better.

You can get it here:

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

Use it like this:

   $ volalign rotated-model.mnc align.xfm aligned-model.mnc

Both align.xfm and aligned-model.mnc are output files.

As part of this you might also then like to align 0,0,0 about the
centre of the volume (or sometimes before), to do this use volcentre:

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

(sorry Nth Americans, you're going to have to learn how to spell, the
fact that we English stole the word from the French is irrelevant)

Use it as such:

   $ volcentre -zero_dircos in.mnc out.mnc

use -help for more options.

Then when you use volalign you can use the -world option so that your
resulting image is centered about the 0,0,0 world co-ordinate.


-- 
Andrew Janke
(a.janke at gmail.com || http://a.janke.googlepages.com/)
Brisbane->Australia    +61 (402) 700 883

From thomas.funck at mail.mcgill.ca  Wed Apr 27 15:59:28 2011
From: thomas.funck at mail.mcgill.ca (Thomas Funck)
Date: Wed, 27 Apr 2011 19:59:28 +0000
Subject: [MINC-users] dynamic memory allocation for hyperslabs
Message-ID: <53F3FD0032C9CC4BA836E8F0FC289065DB90@EXMBX2010-2.campus.MCGILL.CA>

Hi,

I'm trying to dynamically allocate memory for a hyperslab, but this always seems to lead to a seg fault.  I used hyper-test.c to try and figure out the problem. The normal hyper-test.c compiles and runs fine, so I changed "dtemp[CX][CY][CZ];" to "double ***dtemp;" and then allocate the necessary memory by doing:

	dtemp=malloc(CX * sizeof(double**));
	for(i=0; i< CX; i++)
	{
	dtemp[i]=malloc(CY * sizeof(double*));
		for(j=0; j < CY; j++)
		{
		dtemp[i][j]=malloc(CZ * sizeof(double) );
		}
	}

However this resulted in a seg fault on the line:

if (fabs(r - dtemp[i][j][k]) > 1.0e-15)

So even though "miget_real_value_hyperslab" returns 0 and says it gets the hyperslab correctly, there seems to be a problem dereferencing "dtemp" when the memory has been dynamically allocated.

Is there something wrong with my C? Or does "miget_real_value_hyperslab" not work correctly for dynamically allocated memory?

Many thanks for any help!

Best,

Thomas

From eskild at gmail.com  Wed Apr 27 16:24:52 2011
From: eskild at gmail.com (Simon Eskildsen)
Date: Wed, 27 Apr 2011 16:24:52 -0400
Subject: [MINC-users] dynamic memory allocation for hyperslabs
In-Reply-To: <53F3FD0032C9CC4BA836E8F0FC289065DB90@EXMBX2010-2.campus.MCGILL.CA>
References: <53F3FD0032C9CC4BA836E8F0FC289065DB90@EXMBX2010-2.campus.MCGILL.CA>
Message-ID: <BANLkTinw-e068qw0UWxOHKrsPL0nSFZTbQ@mail.gmail.com>

Hi Thomas,

If you want to dynamically allocate a 3D array, I would recommend
doing something like the code below to avoid multiple allocations in
for loops. Not sure if it solves your problem though.

Best,
Simon


dtemp = alloc_3d_double(CX, CY, CZ);

...given the function:

double ***alloc_3d_double(int n1, int n2, int n3)
{
    double ***iii, **ii, *i;
    int j;

    iii = (double ***) calloc(n1,sizeof(double **));
    alloc_error_check(iii);
    ii = (double **) calloc(n1 * n2,sizeof(double *));
    alloc_error_check(ii);
    iii[0] = ii;
    for (j = 1; j < n1; j++) {
        iii[j] = iii[j - 1] + n2;
    }
    i = (double *) calloc(n1 * n2 * n3,sizeof(double));
    alloc_error_check(i);
    ii[0] = i;
    for (j = 1; j < n1 * n2; j++) {
        ii[j] = ii[j - 1] + n3;
    }
    return iii;
}

...and the definition:


#define alloc_error_check(p) { \
    if ((p) == NULL) { \
        fprintf(stderr, "ERROR! Allocation failure. Probably out of
memory.\n"); \
        exit(1); \
    } \
}

On Wed, Apr 27, 2011 at 3:59 PM, Thomas Funck
<thomas.funck at mail.mcgill.ca> wrote:
> Hi,
>
> I'm trying to dynamically allocate memory for a hyperslab, but this always seems to lead to a seg fault. ?I used hyper-test.c to try and figure out the problem. The normal hyper-test.c compiles and runs fine, so I changed "dtemp[CX][CY][CZ];" to "double ***dtemp;" and then allocate the necessary memory by doing:
>
> ? ? ? ?dtemp=malloc(CX * sizeof(double**));
> ? ? ? ?for(i=0; i< CX; i++)
> ? ? ? ?{
> ? ? ? ?dtemp[i]=malloc(CY * sizeof(double*));
> ? ? ? ? ? ? ? ?for(j=0; j < CY; j++)
> ? ? ? ? ? ? ? ?{
> ? ? ? ? ? ? ? ?dtemp[i][j]=malloc(CZ * sizeof(double) );
> ? ? ? ? ? ? ? ?}
> ? ? ? ?}
>
> However this resulted in a seg fault on the line:
>
> if (fabs(r - dtemp[i][j][k]) > 1.0e-15)
>
> So even though "miget_real_value_hyperslab" returns 0 and says it gets the hyperslab correctly, there seems to be a problem dereferencing "dtemp" when the memory has been dynamically allocated.
>
> Is there something wrong with my C? Or does "miget_real_value_hyperslab" not work correctly for dynamically allocated memory?
>
> Many thanks for any help!
>
> Best,
>
> Thomas
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From a.janke at gmail.com  Wed Apr 27 19:11:26 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 28 Apr 2011 09:11:26 +1000
Subject: [MINC-users] dynamic memory allocation for hyperslabs
In-Reply-To: <53F3FD0032C9CC4BA836E8F0FC289065DB90@EXMBX2010-2.campus.MCGILL.CA>
References: <53F3FD0032C9CC4BA836E8F0FC289065DB90@EXMBX2010-2.campus.MCGILL.CA>
Message-ID: <BANLkTikeEc3Yogm1diLB5Eqgtx9taddofQ@mail.gmail.com>

Hi Thomas,

On Thu, Apr 28, 2011 at 05:59, Thomas Funck <thomas.funck at mail.mcgill.ca> wrote:
> I'm trying to dynamically allocate memory for a hyperslab, but this always seems to lead to a seg fault. ?I used hyper-test.c to try and figure out the problem. The normal hyper-test.c compiles and runs fine, so I changed "dtemp[CX][CY][CZ];" to "double ***dtemp;" and then allocate the necessary memory by doing:
>
> ? ? ? ?dtemp=malloc(CX * sizeof(double**));
> ? ? ? ?for(i=0; i< CX; i++)
> ? ? ? ?{
> ? ? ? ?dtemp[i]=malloc(CY * sizeof(double*));
> ? ? ? ? ? ? ? ?for(j=0; j < CY; j++)
> ? ? ? ? ? ? ? ?{
> ? ? ? ? ? ? ? ?dtemp[i][j]=malloc(CZ * sizeof(double) );
> ? ? ? ? ? ? ? ?}
> ? ? ? ?}
>
> However this resulted in a seg fault on the line:
>
> if (fabs(r - dtemp[i][j][k]) > 1.0e-15)
>
> So even though "miget_real_value_hyperslab" returns 0 and says it gets the hyperslab correctly, there seems to be a problem dereferencing "dtemp" when the memory has been dynamically allocated.
>
> Is there something wrong with my C? Or does "miget_real_value_hyperslab" not work correctly for dynamically allocated memory?

miget_real_value_hyperslab does work for dynamically allocated memory,
but I dont think you are doing what you want to be...
miget_real_value_hyperslab is expecting a pointer to a memory buffer
that will be then indexed as per a "normal" multidimensional array.
see:

   http://pw1.netcom.com/~tjensen/ptr/ch7x.htm

or

   http://en.wikibooks.org/wiki/C_Programming/Arrays

for an explanation of how in C array[x][y] is really just *(*(array + x) + y)

What you are allocating is an array of pointers to arrays pointers to
arrays.  (Here's hoping I got my grammar right there!). If you want to
dynamically allocate the array you can either do a single malloc

   buf = malloc(sizeof(double) * CX * CY * CZ)

or take advantage of being able to declare arrays within blocks:

   int somefunction(int CX, int CY, int CZ){
      array[CX][CY][CZ];

      ...

   }

The reason your array of pointers to arrays or pointers to arrays
doesn't work as you'd expect is that miget_real_value_hyperslab will
be attempting to stuff the entire hyperslabs values into the first
array of pointers (ie: in dtemp), which is nothing more than array of
double* of length CX. Odds are this will work at runtime as C doesn't
do much bounds checking and odds are the memory you are allocating for
the sub-arrays will be right after dtemp so things will probably work
90% of the time. When you go to access the elements though things may
well break.

Hope that helps, I could be wrong with the above but this is what I
can guess from the code and info you have sent so far.

ta


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Andrew Janke
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