From andrew at biospective.com  Wed Apr  4 11:35:54 2018
From: andrew at biospective.com (Andrew Wood)
Date: Wed, 4 Apr 2018 11:35:54 -0400
Subject: [MINC-users] Surface Segmentation with Display
Message-ID: <CABApf9Ffpw6PY6BR382F0yttCzSCZBkvff7NCVtxmZb4fR0+gw@mail.gmail.com>

Hi all,

Is thee a tutorial out there that shows how to operate Display's surface
segmentation capabilities? I've been doing a workflow that is probably more
cumbersome than it ought to be:

1) load the surface object and volumetric labels
2) paint on the volume
3) intersect the surface with the volumetric labels
4) If the surface segmentation looks good, then great; else go back to 2.

I see that Display has surface segmentation features, but I can't figure
out how to use them. The end goal is to generate per-vertex integer labels,
either directly written into the .obj file (to be externally extracted to a
.txt file) or saved out of Display directly.

Thanks,
Andrew

From bert at phalarope.com  Fri Apr  6 22:31:38 2018
From: bert at phalarope.com (Robert D. Vincent)
Date: Fri, 6 Apr 2018 22:31:38 -0400
Subject: [MINC-users] Surface Segmentation with Display
In-Reply-To: <CABApf9Ffpw6PY6BR382F0yttCzSCZBkvff7NCVtxmZb4fR0+gw@mail.gmail.com>
References: <CABApf9Ffpw6PY6BR382F0yttCzSCZBkvff7NCVtxmZb4fR0+gw@mail.gmail.com>
Message-ID: <CAAd5DeSga6T0O4t-DobTd+ty-L_nTqs6EuBkaHrX3S4x8sFfHw@mail.gmail.com>

Hi Andrew,

Sorry for the delay in responding.

Unfortunately, the current implementation of surface segmentation does not
work with integer labels like the volumetric labeling.. It allows you to
paint colors on the surface on a number of polygons under the mouse cursor.
Once you've done this, you can save the colored image. I'm not certain what
the intended workflow or even the intended purpose. It would be fairly easy
to add support for integer labeling of the surface similar to what is
currently done in the volume. There are already provisions to allow you to
load, display, and save per-vertex data, so it's just a question of making
it possible to create and edit the vertex data.

Email me directly if you want to discuss and perhaps we can make something
you'll find useful.

    -bert

On Wed, Apr 4, 2018 at 11:35 AM, Andrew Wood <andrew at biospective.com> wrote:

> Hi all,
>
> Is thee a tutorial out there that shows how to operate Display's surface
> segmentation capabilities? I've been doing a workflow that is probably more
> cumbersome than it ought to be:
>
> 1) load the surface object and volumetric labels
> 2) paint on the volume
> 3) intersect the surface with the volumetric labels
> 4) If the surface segmentation looks good, then great; else go back to 2.
>
> I see that Display has surface segmentation features, but I can't figure
> out how to use them. The end goal is to generate per-vertex integer labels,
> either directly written into the .obj file (to be externally extracted to a
> .txt file) or saved out of Display directly.
>
> Thanks,
> Andrew
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From matthew at biospective.com  Mon Apr  9 14:42:16 2018
From: matthew at biospective.com (Matthew Lee)
Date: Mon, 9 Apr 2018 14:42:16 -0400
Subject: [MINC-users] Map of dicom tags to minc header
Message-ID: <CADxcC9f7xXRbGDceCkF-bSbM-auUZeHeyWj7Hy=R45QjeOeVag@mail.gmail.com>

Hi All,

Is there a map somewhere showing which DICOM tags are mapped to MINC
headers?  I have some DICOM data with specific tags that I need to keep
track of, but it isn't always clear what the equivalent MINC header field
is, especially with how some tags are converted into named variable
attributes, and others are saved based on the DICOM tag number.

Thanks,

Matthew

From gabriel.devenyi at mcgill.ca  Mon Apr  9 15:14:58 2018
From: gabriel.devenyi at mcgill.ca (Gabriel A. Devenyi)
Date: Mon, 9 Apr 2018 15:14:58 -0400
Subject: [MINC-users] Map of dicom tags to minc header
In-Reply-To: <be4623456c034458b285f08b9486f9bf@YQXPR0101MB1734.CANPRD01.PROD.OUTLOOK.COM>
References: <be4623456c034458b285f08b9486f9bf@YQXPR0101MB1734.CANPRD01.PROD.OUTLOOK.COM>
Message-ID: <CAFQOoOpG=6rjDUFmLovJYOBBrT5oc6Mu1fv85xE3r-Z2oRq-5g@mail.gmail.com>

Hi Matthew,

No need to worry about ?mapping?. THe exact dicom header values are encoded
into the header in addition to conversion in various places:

Example

    int dicom_0x0051 ;
        dicom_0x0051:el_0x1008 = "IMAGE NUM 4 " ;
        dicom_0x0051:el_0x0010 = "SIEMENS MR HEADER " ;
        dicom_0x0051:vartype = "group________" ;
        dicom_0x0051:el_0x100f = "C:HEA;HEP " ;
        dicom_0x0051:el_0x1013 = "+LPH" ;
        dicom_0x0051:el_0x0000 = 14b, 1b, 0b, 0b ;
        dicom_0x0051:el_0x1017 = "SL 1.0" ;
        dicom_0x0051:el_0x100e = "Sag>Tra(-2.1)>Cor(-0.5) " ;
        dicom_0x0051:el_0x1012 = "TP 0" ;
        dicom_0x0051:el_0x1011 = "p2" ;
        dicom_0x0051:el_0x100a = "TA 05:10" ;
        dicom_0x0051:el_0x1009 = "1.0 " ;
        dicom_0x0051:el_0x100d = "SP L87.1" ;
        dicom_0x0051:el_0x1015 = "D/R " ;
        dicom_0x0051:el_0x1016 = "p2 M/ND/NORM" ;
        dicom_0x0051:el_0x100c = "FoV 240*256 " ;
        dicom_0x0051:varid = "MNI DICOM variable" ;
        dicom_0x0051:el_0x100b = "240*256 " ;
        dicom_0x0051:el_0x1019 = "A1/IR " ;

?

On Mon, Apr 9, 2018 at 2:42 PM, Matthew Lee <matthew at biospective.com> wrote:

> Hi All,
>
> Is there a map somewhere showing which DICOM tags are mapped to MINC
> headers?  I have some DICOM data with specific tags that I need to keep
> track of, but it isn't always clear what the equivalent MINC header field
> is, especially with how some tags are converted into named variable
> attributes, and others are saved based on the DICOM tag number.
>
> Thanks,
>
> Matthew
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From pierre.bellec at criugm.qc.ca  Fri Apr 13 13:33:14 2018
From: pierre.bellec at criugm.qc.ca (Pierre Bellec)
Date: Fri, 13 Apr 2018 13:33:14 -0400
Subject: [MINC-users] Brainhack MTL 2018
Message-ID: <CADPHwxBxjLgwScbLi8PD6m0zV1-9LAgVxGcXGb04aGH9uAxmrg@mail.gmail.com>

Dear MINC users,

The 2018 edition of Brainhack Montreal
<https://brainhackmtl.github.io/global2018/> will bring together
researchers with disparate backgrounds to collaborate on open science
projects in neuroimaging. Brainhack Montreal 2018 is part of the Brainhack
Global 2018 <http://www.brainhack.org/global2018/>, with simultaneous
hackathons running at more than 30 sites across the globe. Participants are
encouraged to post project ideas on the website of brainhack Montreal.

*Dates*: April 26th-27th, 2018
*Costs*: $30 CAD, includes onsite breakfast and lunch for two days
*Location*: Centre de Recherche de l?Institut Universitaire de G?riatrie de
Montr?al (CRIUGM), Montr?al, Canada.
*Website*: https://brainhack101.github.io/mtl-brainhack-2018

Brainhack Montreal is grateful for the support of the Qu?bec BioImaging
Network. <https://www.rbiq-qbin.qc.ca/Home>

Best regards,

Pierre Bellec
Assistant professor/Professeur adjoint sous octroi, D?partement
d'informatique et de recherche op?rationnelle (DIRO
<http://diro.umontreal.ca/>)
Director/Directeur, Unit? de Neuroimagerie Fonctionnelle (UNF
<http://unf-montreal.ca>)
Researcher/Chercheur Centre de recherche de l'institut Universitaire de
g?riatrie de Montr?al (CRIUGM <http://www.criugm.qc.ca/>)
Universit? de Montr?al, Montr?al, Canada
Phone +1 514 713 5596
Coordinates/c <http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec>
oordonn?es <http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec>.
Laboratory/Laboratoire SIMEXP <http://simexp-lab.org>.

From gabriel.devenyi at mcgill.ca  Fri Apr 13 16:01:57 2018
From: gabriel.devenyi at mcgill.ca (Gabriel A. Devenyi)
Date: Fri, 13 Apr 2018 16:01:57 -0400
Subject: [MINC-users] Sampling a volume with a tag file?
Message-ID: <CAFQOoOrA0fYVokmnPodJTabAi48EbGJpz5Cog8Y6Oq6vpw24Lw@mail.gmail.com>

Hi minc-users,

I have a tag file with point coordinates that I'd like to use to sample the
value of a volume at the closest voxel for each point.

I can't find an immediately obvious command for this, does one exist?

Thanks!

--
Gabriel A. Devenyi B.Eng. 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

From vladimir.fonov at gmail.com  Fri Apr 13 16:09:24 2018
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Fri, 13 Apr 2018 16:09:24 -0400
Subject: [MINC-users] Sampling a volume with a tag file?
In-Reply-To: <CAFQOoOrA0fYVokmnPodJTabAi48EbGJpz5Cog8Y6Oq6vpw24Lw@mail.gmail.com>
References: <CAFQOoOrA0fYVokmnPodJTabAi48EbGJpz5Cog8Y6Oq6vpw24Lw@mail.gmail.com>
Message-ID: <18a045b3-aa21-f970-0165-888d8b9e20ae@gmail.com>

Hello,


 > tagtominc input.mnc input.tag mask.mnc

 > mincsample input.mnc -mask mask.mnc


On 2018-04-13 04:01 PM, Gabriel A. Devenyi wrote:
> Hi minc-users,
> 
> I have a tag file with point coordinates that I'd like to use to sample the
> value of a volume at the closest voxel for each point.
> 
> I can't find an immediately obvious command for this, does one exist?
> 
> Thanks!
> 
> --
> Gabriel A. Devenyi B.Eng. 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
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> 


-- 
Best regards,

  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com