From zijdenbos at gmail.com  Wed Apr  3 10:54:57 2019
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Wed, 3 Apr 2019 10:54:57 -0400
Subject: [MINC-users] Time frame start values
In-Reply-To: <CAAd5DeSW2n6iUmb6bGxT65LJvy529rtXyv+nP_EC+S6btgZfdQ@mail.gmail.com>
References: <CABEEk17BUixj1=O3dSZCahrvD6z0FKXWSQ1G0GnQvdPQ-Sy5NQ@mail.gmail.com>
 <CAAd5DeRwvQJVOO0mqn0_wGL2ZE_nVfFo9VRmeLCQ_Co95ReXNw@mail.gmail.com>
 <CANHs=MfN8+iebZu1i3ryYk0WzuST=gc-XJPKcKkWvWt0vWBmJQ@mail.gmail.com>
 <CAAd5DeSW2n6iUmb6bGxT65LJvy529rtXyv+nP_EC+S6btgZfdQ@mail.gmail.com>
Message-ID: <CABEEk14xnKumfQ0j=9wX31U2cVtmwCJpGoMCw6NyAtZT6FL2QQ@mail.gmail.com>

Hi Bert - thanks much for your help with this! We'll look at it and get
back to you. The PET time dimension is obviously not as clear-cut as I once
thought it was :-}

-- A

On Sun, Mar 31, 2019 at 12:48 PM Robert D. Vincent <bert at phalarope.com>
wrote:

> Hi Alex,
>
> I may have solved some of these issues - I just pushed a few small updates
> to github.
>
> With at least some of the PET data I have, using the Acquisition time field
> is useful for the PET timings, although it produces a non-zero start value
> in most cases.
>
> Also I found and fixed a bug where we incorporated Siemens proprietary
> information into the PET DICOM, but our Siemens-specific code is only
> correct when used with MR data.
>
> Please try these out and let me know if you're still having problems.
>
>     -bert
>
> On Fri, Mar 29, 2019 at 4:39 PM Jean-Philippe Coutu <jp at biospective.com>
> wrote:
>
> > Hi Robert,
> >
> > I like your idea of using the frame widths, and I just wanted to mention
> > one caveat we stumbled upon recently, where this might not work. We have
> > had to convert a dataset where the time frames were not contiguous, and
> > therefore there were effectively missing time frames. I think this is
> > unusual and maybe dcm2mnc should not be expected to be able to convert
> > that, but I just thought I would mention it. I think having this option
> you
> > suggest would definitely be good for this case though.
> >
> > We have been fixing up 4D cases for a while now, which largely seem to
> have
> > issues in get_file_indices(), mostly because of what you stated: unusual
> > worthlessness of certain dicom fields for certain situations/scanners.
> > Basically there is no ideal order of prioritisation for which dicom tags
> > are always more reliable than other when it comes to finding time indices
> > (and also all sorts of range-checking issues). We haven't made pull
> > requests for those changes yet because I think we need to reorganise
> them a
> > bit better.
> >
> > Best,
> > JP
> >
> > On Thu, Mar 28, 2019 at 9:42 AM Robert D. Vincent <bert at phalarope.com>
> > wrote:
> >
> > > Hi Alex,
> > >
> > > I've heard of these issues in a number of instances, I am (slowly, when
> > > time permits) trying to resolve one particular case in dcm2mnc.
> > >
> > > PET files often use the DICOM field 0054:1300, the "Frame Reference
> > Time",
> > > as the main (or only) indication of PET frame start times. However, as
> > you
> > > can see at the link I have provided, the exact meaning of this field is
> > > undefined, so it is unusually worthless even for DICOM. Some PET
> > sequences
> > > use other fields to indicate the frame times, but consistency here is
> > poor.
> > >
> > > https://www.dabsoft.ch/dicom/3/C.8.9.4.1.5/
> > >
> > > My intended solution is to use the frame widths ("Actual Frame
> Duration",
> > > 0018:1242) to reconstruct the MINC dimension by simply setting the
> start
> > > time of each frame to the sum of the preceding frame widths. This
> relies
> > on
> > > the accuracy of these frame widths, but in my experience this may be
> more
> > > reliable than relying on the frame times. However, if the frame times
> are
> > > somehow meaningful, that information will be lost (or at least not
> stored
> > > in a standard place). So my plan is to make this depend on a command
> line
> > > option.
> > >
> > >     -bert
> > >
> > > On Thu, Mar 28, 2019 at 9:15 AM Alex Zijdenbos <zijdenbos at gmail.com>
> > > wrote:
> > >
> > > > Hello all,
> > > >
> > > > I've running into an issue I don't know what to do with (yet). How
> are
> > > (or
> > > > should) start values be interpreted in a MINC time-dimension?
> > > >
> > > > For spatial dimensions, the voxel positions are in the center of the
> > > voxel;
> > > > but in converting dynamic PET data from various scanners, we are
> seeing
> > > > what looks like variations between scanners in terms of whether the
> > start
> > > > is center-frame, or start-of-frame.
> > > >
> > > > We also sometimes end up with negative time steps out of dcm2mnc,
> which
> > > > calls into question whether (a) that should ever happen; and (b) how
> > for
> > > > example mincreshape behaves when re-ordering that dimension. My
> > > assumption
> > > > is that mincreshape will interpret the start to be center-frame, and
> > that
> > > > therefore changing the sign of the time-step might end up with a
> wrong
> > > > start value.
> > > >
> > > > If anybody has thoughts about or experience with these issues, please
> > > share
> > > > :-)
> > > >
> > > > Thanks,
> > > >
> > > > -- A
> > > > _______________________________________________
> > > > MINC-users at bic.mni.mcgill.ca
> > > > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > > >
> > > _______________________________________________
> > > MINC-users at bic.mni.mcgill.ca
> > > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > >
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From colm.mcginnity at kcl.ac.uk  Mon Apr 15 09:59:42 2019
From: colm.mcginnity at kcl.ac.uk (McGinnity, Colm)
Date: Mon, 15 Apr 2019 13:59:42 +0000
Subject: [MINC-users] Mincview and register launch issues
Message-ID: <AM6PR03MB36705698034167526BB3199BC52B0@AM6PR03MB3670.eurprd03.prod.outlook.com>

Dear Minc Users,

I am new to the Minc toolkit, and was wondering if anyone could help me with these little issues:


1.       Mincview yields these errors:
"Dimensions of start or count vectors not equal to dimensions in file"; "Unknown argument: -monitor".


2.       Register seems to open ok when I launch it from my Ubuntu desktop, but when I try to open it remotely via MobaXterm (from Windows) I get:
"X Error of failed request:  BadRequest (invalid request code or no such operation)
  Major opcode of failed request:  146 (GLX)
  Minor opcode of failed request:  168 ()
  Serial number of failed request:  39
  Current serial number in output stream:  39"

Does anyone have any suggestions? I apologise if these issues have already been answered in another email thread.
Many thanks and best wishes,
Colm

Colm J. McGinnity MBChB PhD
School of Biomedical Engineering & Imaging Sciences
King's College London
& KCL/GSTT PET Centre
4th Floor Lambeth Wing
St. Thomas' Hospital
Westminster Bridge Road
London SE1 7EH
colm.mcginnity at kcl.ac.uk<mailto:colm.mcginnity at kcl.ac.uk>
020-7188-9259


From bert at phalarope.com  Tue Apr 16 07:38:40 2019
From: bert at phalarope.com (Robert D. Vincent)
Date: Tue, 16 Apr 2019 07:38:40 -0400
Subject: [MINC-users] Mincview and register launch issues
In-Reply-To: <AM6PR03MB36705698034167526BB3199BC52B0@AM6PR03MB3670.eurprd03.prod.outlook.com>
References: <AM6PR03MB36705698034167526BB3199BC52B0@AM6PR03MB3670.eurprd03.prod.outlook.com>
Message-ID: <CAAd5DeTFY3G+6pDk3WudfMQ4ax8frMEFzDr52WwDeOA225hx=Q@mail.gmail.com>

Hi Colm,

1. One possibility is that the mincview script relies on ImageMagick's
"display" command. I have heard elsewhere that the latest version of
ImageMagick might break some scripts. What do you see if you type "display
--version" at your command prompt?

2. I know that register does not work reliably over a remote X session -
I'm not certain why, but the errors suggest that the link can't handle some
of the OpenGL-related messages.

    -bert

On Mon, Apr 15, 2019 at 10:01 AM McGinnity, Colm <colm.mcginnity at kcl.ac.uk>
wrote:

> Dear Minc Users,
>
> I am new to the Minc toolkit, and was wondering if anyone could help me
> with these little issues:
>
>
> 1.       Mincview yields these errors:
> "Dimensions of start or count vectors not equal to dimensions in file";
> "Unknown argument: -monitor".
>
>
> 2.       Register seems to open ok when I launch it from my Ubuntu
> desktop, but when I try to open it remotely via MobaXterm (from Windows) I
> get:
> "X Error of failed request:  BadRequest (invalid request code or no such
> operation)
>   Major opcode of failed request:  146 (GLX)
>   Minor opcode of failed request:  168 ()
>   Serial number of failed request:  39
>   Current serial number in output stream:  39"
>
> Does anyone have any suggestions? I apologise if these issues have already
> been answered in another email thread.
> Many thanks and best wishes,
> Colm
>
> Colm J. McGinnity MBChB PhD
> School of Biomedical Engineering & Imaging Sciences
> King's College London
> & KCL/GSTT PET Centre
> 4th Floor Lambeth Wing
> St. Thomas' Hospital
> Westminster Bridge Road
> London SE1 7EH
> colm.mcginnity at kcl.ac.uk<mailto:colm.mcginnity at kcl.ac.uk>
> 020-7188-9259
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From vladimir.fonov at gmail.com  Tue Apr 16 10:23:48 2019
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Tue, 16 Apr 2019 10:23:48 -0400
Subject: [MINC-users] Mincview and register launch issues
In-Reply-To: <CAAd5DeTFY3G+6pDk3WudfMQ4ax8frMEFzDr52WwDeOA225hx=Q@mail.gmail.com>
References: <AM6PR03MB36705698034167526BB3199BC52B0@AM6PR03MB3670.eurprd03.prod.outlook.com>
 <CAAd5DeTFY3G+6pDk3WudfMQ4ax8frMEFzDr52WwDeOA225hx=Q@mail.gmail.com>
Message-ID: <CAMCwi7OQ4ZMX22uU9NkwwQ6NdcC0sd2V4TVv2AAxY-e7S=905g@mail.gmail.com>

Hello,

regarding issue number 2 , I have seen numerous problems with GLX over SSH
, I am not sure how to fix them.
For example: ssh -X -Y from CentoOS 6 to Ubuntu 18.04 - register & display
works, ssh -X -Y from Ubuntu 18.04 to Ubuntu 18.04 (different computers)  -
register and display doesn't work, ssh from Ubuntu 18.04 to itself
(localhost) - works.
You can try to diagnose the problem using glxinfo and glxgears  (
mesa-utils package on Ubuntu)


On Tue, 16 Apr 2019 at 07:39, Robert D. Vincent <bert at phalarope.com> wrote:

> Hi Colm,
>
> 1. One possibility is that the mincview script relies on ImageMagick's
> "display" command. I have heard elsewhere that the latest version of
> ImageMagick might break some scripts. What do you see if you type "display
> --version" at your command prompt?
>
> 2. I know that register does not work reliably over a remote X session -
> I'm not certain why, but the errors suggest that the link can't handle some
> of the OpenGL-related messages.
>
>     -bert
>
> On Mon, Apr 15, 2019 at 10:01 AM McGinnity, Colm <colm.mcginnity at kcl.ac.uk
> >
> wrote:
>
> > Dear Minc Users,
> >
> > I am new to the Minc toolkit, and was wondering if anyone could help me
> > with these little issues:
> >
> >
> > 1.       Mincview yields these errors:
> > "Dimensions of start or count vectors not equal to dimensions in file";
> > "Unknown argument: -monitor".
> >
> >
> > 2.       Register seems to open ok when I launch it from my Ubuntu
> > desktop, but when I try to open it remotely via MobaXterm (from Windows)
> I
> > get:
> > "X Error of failed request:  BadRequest (invalid request code or no such
> > operation)
> >   Major opcode of failed request:  146 (GLX)
> >   Minor opcode of failed request:  168 ()
> >   Serial number of failed request:  39
> >   Current serial number in output stream:  39"
> >
> > Does anyone have any suggestions? I apologise if these issues have
> already
> > been answered in another email thread.
> > Many thanks and best wishes,
> > Colm
> >
> > Colm J. McGinnity MBChB PhD
> > School of Biomedical Engineering & Imaging Sciences
> > King's College London
> > & KCL/GSTT PET Centre
> > 4th Floor Lambeth Wing
> > St. Thomas' Hospital
> > Westminster Bridge Road
> > London SE1 7EH
> > colm.mcginnity at kcl.ac.uk<mailto:colm.mcginnity at kcl.ac.uk>
> > 020-7188-9259
> >
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> _______________________________________________
> 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