From zijdenbos at gmail.com  Fri Jun  4 15:22:53 2021
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Fri, 4 Jun 2021 15:22:53 -0400
Subject: [MINC-users] Odd behaviour with recent versions of
	dcm2mnc/mincreshape
In-Reply-To: <CABEEk15UtSb=8saHJ-iFTk_usWijNf1oQrNv5OM0-P92pWiiqQ@mail.gmail.com>
References: <CABEEk15UtSb=8saHJ-iFTk_usWijNf1oQrNv5OM0-P92pWiiqQ@mail.gmail.com>
Message-ID: <CABEEk155yLRC92EqWZNkn==zQmrRfp0np+8aT4bbNkw8gVv=Nw@mail.gmail.com>

Followup: we found a simpler way to demonstrate this issue:

$ make_phantom in.mnc && mincreshape in.mnc out.mnc && mincinfo -attvalue
xspace:spacing -attvalue yspace:spacing -attvalue zspace:spacing out.mnc
Copying
chunks:................................................................................................................................Done.
zspace
zspace
zspace

Massina Yahia will also pull-request a fix for this in the near future.

Have a good weekend! :-)

-- Alex

On Mon, May 31, 2021 at 11:30 PM Alex Zijdenbos <zijdenbos at gmail.com> wrote:

> Hi all,
>
> Stumbled into something rather strange:
>
> $ dcm2mnc DICOM/ADNI_126_S_0709_MR_IR-FSPGR-Repeat MINC_dcm2mnc_2.3.01
> $ mincheader MINC_dcm2mnc_2.3.01/*/*mnc | grep spacing
> xspace:spacing = "regular__" ;
> yspace:spacing = "regular__" ;
> zspace:spacing = "regular__" ;
> $ mincreshape MINC_dcm2mnc_2.3.01/*/*mnc MINC_dcm2mnc_2.3.01/reshaped.mnc
> $ mincheader MINC_dcm2mnc_2.3.01/reshaped.mnc | grep spacing
> xspace:spacing = "yspace" ;
> yspace:spacing = "yspace" ;
> zspace:spacing = "yspace" ;
>
> In other words, the <dim>:spacing attribute gets mangled by what *should*
> be a no-op. This is using:
> $ dcm2mnc -version
> program: 2.3.01 built Dec 10 2020 01:01:35
> libminc: 2.4.03
> netcdf : 4.5.0 of Jun 26 2018 10:58:21 $
> HDF5   : 1.8.20
>
> If I do the exact same thing with this older version:
> $ dcm2mnc -version
> program: 2.0.07 built Mar 19 2014 16:54:51
> libminc: 2.2.00
> netcdf : 3.6.1 of Mar 19 2014 16:53:18 $
> HDF5   : 1.8.9
>
> All seems to work as expected (all :spacing attributes remain
> "regular__"). Doing a quick comparison of the headers of the MINC volumes
> generated by these two versions of dcm2mnc, a few differences appear:
> $ diff <( mincheader MINC_dcm2mnc_2.0.07/*/*.mnc | grep spac | sort) <(
> mincheader MINC_dcm2mnc_2.3.01/*/*.mnc | grep spac | sort)
> 3c3
> < double xspace(xspace) ;
> ---
> > double xspace ;
> 10d9
> <  xspace = -100.899, -99.6994, -98.4994, -97.2994, -96.0994, -94.8994,
> 11a11
> >  xspace = 97.1005 ;
> 14d13
> < xspace:dimorder = "xspace" ;
>
> Further, if I use the "new" mincreshape on the "old" volume or vice versa,
> the spacing attributes remain "regular__". It's only the combination of
> both "new" dcm2mnc and "new" mincreshape that results in this.
>
> Unfortunately I can't actually distribute the source data, but it is ADNI
> data, and this is not an isolated case - this pretty much happens on most
> volumes that I pick up.
>
> Anybody any idea what we might be looking at here?
>
> Thanks,
>
> -- A
>

From sean at rogue-research.com  Wed Jun 23 14:27:43 2021
From: sean at rogue-research.com (Sean McBride)
Date: Wed, 23 Jun 2021 14:27:43 -0400
Subject: [MINC-users] Can MINC tools be used to crop a dataset?
Message-ID: <20210623182743.387507594@mail.rogue-research.com>

Hi MINC users,

I only know how to do one or two simple things with MINC tools, but now I'm looking to do something a bit more complex, and I'm hoping someone can point me in the right direction.

I have a huge dataset that, on account of its hugeness, is slow to deal with.  But in fact most of the voxels are just emptiness.  Is it possible for me to specify a range in x,y,z of voxels that I want to keep and then create a new smaller MINC file?

Thanks,

Sean




From claude at bic.mni.mcgill.ca  Wed Jun 23 14:37:55 2021
From: claude at bic.mni.mcgill.ca (Claude LEPAGE)
Date: Wed, 23 Jun 2021 14:37:55 -0400
Subject: [MINC-users] Can MINC tools be used to crop a dataset?
In-Reply-To: <20210623182743.387507594@mail.rogue-research.com>
Message-ID: <202106231837.15NIbtKC016944@login1.bic.mni.mcgill.ca>

Hi Sean,

I feel I know an answer for this.

% mincbbox -help

Command-specific options:
 -threshold:     Real value threshold for bounding box.
		Default value: 0
 -one_line:      Output on one line (default): start_x y z width_x y z
 -two_lines:     Output on two lines: start_x y z \n width_x y z
 -mincresample:  Output format for mincresample: (-step x y z -start x y z -nelements x y z
 -mincreshape:   Output format for mincreshape: (-start x,y,z -count dx,dy,dz
 -minccrop:      Output format for minccrop: (-xlim x1 x2 -ylim y1 y2 -zlim z1 z2
Options for logging progress. Default = -verbose.
 -verbose:       Write messages indicating progress
 -quiet:         Do not write log messages
 -debug:         Print out debug info.
Generic options for all commands:
 -help:          Print summary of command-line options and abort
 -version:       Print version number of program and exit

Usage: mincbbox [<options>] <inputfile> 
       mincbbox [-help]

You can use it in combination with -threshold and output the instructions
for use with mincresample, mincreshape or minccrop. I'll let you discover
the details. After that, I would suggest a bit of padding around the part
of the image that you want to keep (autocrop -extend).

Claude


>
> Hi MINC users,
>
> I only know how to do one or two simple things with MINC tools, but now I'm looking to do something a bit more complex, and I'm hoping someone can point me in the right direction.
>
> I have a huge dataset that, on account of its hugeness, is slow to deal with.  But in fact most of the voxels are just emptiness.  Is it possible for me to specify a range in x,y,z of voxels that I want to keep and then create a new smaller MINC file?
>
> Thanks,
>
> Sean
>