From colm.mcginnity at kcl.ac.uk  Fri May 28 09:56:24 2021
From: colm.mcginnity at kcl.ac.uk (McGinnity, Colm)
Date: Fri, 28 May 2021 13:56:24 +0000
Subject: [MINC-users] mnc2nii floating point exception
Message-ID: <VE1PR03MB5424AD7A4A3A0DE86BEE1A1CC5229@VE1PR03MB5424.eurprd03.prod.outlook.com>

Dear Experts,

I am getting a 'Floating point exception' error when trying to convert a 4D .mnc file to a .nii file using mnc2nii. Can anyone tell me how to fix this, please?
Thanks and best wishes,
Colm



From gabriel.devenyi at mcgill.ca  Fri May 28 10:00:44 2021
From: gabriel.devenyi at mcgill.ca (Gabriel A. Devenyi)
Date: Fri, 28 May 2021 10:00:44 -0400
Subject: [MINC-users] mnc2nii floating point exception
In-Reply-To: <VE1PR03MB5424AD7A4A3A0DE86BEE1A1CC5229@VE1PR03MB5424.eurprd03.prod.outlook.com>
References: <VE1PR03MB5424AD7A4A3A0DE86BEE1A1CC5229@VE1PR03MB5424.eurprd03.prod.outlook.com>
Message-ID: <CAFQOoOr=rnpiaj0pkH9wmeSoe+kjy+ZDaHGD=H9z_nJo6koZUg@mail.gmail.com>

Hi,

Can you please open an issue with full technical details at
https://github.com/BIC-MNI/minc-tools

--------------------------------------------------------
Asking for technical help? Get help fast:
https://www.chiark.greenend.org.uk/~sgtatham/bugs.html
http://www.catb.org/~esr/faqs/smart-questions.html#beprecise
https://en.wikipedia.org/wiki/XY_problem
https://stackoverflow.com/help/minimal-reproducible-example


--
Gabriel A. Devenyi Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
Affiliate, Department of Psychiatry
McGill University
t: 514.761.6131x4781
e: gabriel.devenyi at mcgill.ca


On Fri, 28 May 2021 at 09:56, McGinnity, Colm <colm.mcginnity at kcl.ac.uk>
wrote:

> Dear Experts,
>
> I am getting a 'Floating point exception' error when trying to convert a
> 4D .mnc file to a .nii file using mnc2nii. Can anyone tell me how to fix
> this, please?
> Thanks and best wishes,
> Colm
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From vladimir.fonov at gmail.com  Fri May 28 14:00:28 2021
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Fri, 28 May 2021 14:00:28 -0400
Subject: [MINC-users] mnc2nii floating point exception
In-Reply-To: <VE1PR03MB5424AD7A4A3A0DE86BEE1A1CC5229@VE1PR03MB5424.eurprd03.prod.outlook.com>
References: <VE1PR03MB5424AD7A4A3A0DE86BEE1A1CC5229@VE1PR03MB5424.eurprd03.prod.outlook.com>
Message-ID: <CAMCwi7NDdnUpBSfKDA5=ZTOQvRu7Pfo3mSOpbvWNLVRmVb_XGg@mail.gmail.com>

Are you using 1.9.18 version of minc-toolkit?
It might have been fixed in https://github.com/BIC-MNI/minc-tools/issues/109

On Fri, May 28, 2021 at 9:57 AM McGinnity, Colm <colm.mcginnity at kcl.ac.uk>
wrote:

> Dear Experts,
>
> I am getting a 'Floating point exception' error when trying to convert a
> 4D .mnc file to a .nii file using mnc2nii. Can anyone tell me how to fix
> this, please?
> Thanks and best wishes,
> Colm
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


-- 
Best regards,

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

From zijdenbos at gmail.com  Mon May 31 23:30:47 2021
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Mon, 31 May 2021 23:30:47 -0400
Subject: [MINC-users] Odd behaviour with recent versions of
	dcm2mnc/mincreshape
Message-ID: <CABEEk15UtSb=8saHJ-iFTk_usWijNf1oQrNv5OM0-P92pWiiqQ@mail.gmail.com>

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