[MINC-users] mincreshape +direction (Alex & Vladimir)
ting guo
jessieguo80 at hotmail.com
Thu Mar 19 12:18:07 EDT 2015
Hi Alex and Vladimir,
Thank you guys for your prompt reply. That helped me solve the problem.
Many thanks,
Jessie
> From: minc-users-request at bic.mni.mcgill.ca
> Subject: MINC-users Digest, Vol 115, Issue 3
> To: minc-users at bic.mni.mcgill.ca
> Date: Wed, 18 Mar 2015 12:00:01 -0400
>
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> Today's Topics:
>
> 1. mincreshape +direction (ting guo)
> 2. Re: mincreshape +direction (Alex Zijdenbos)
> 3. IT position in neuroimaging at University of Calgary (Oury Monchi)
> 4. Re: mincreshape +direction (Vladimir S. FONOV)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 18 Mar 2015 05:22:10 +0800
> From: ting guo <jessieguo80 at hotmail.com>
> To: "minc-users at bic.mni.mcgill.ca" <minc-users at bic.mni.mcgill.ca>
> Subject: [MINC-users] mincreshape +direction
> Message-ID: <COL128-W721459447421CECAEA4E0B9030 at phx.gbl>
> Content-Type: text/plain; charset="gb2312"
>
> Dear Minc Users,
> I was trying to use mincreshape to flip a image to give positive yspace, but it didn't work. The following are what I did and what I got as results. As you can see, the image remains unchanged. Am I missing certain important options? How can I flip the image and have positive yspace? I would really appreciate your suggestions.
> Thank you very much!
> Jessie
> $ mincinfo ImageA.mnc
>
>
>
>
>
>
>
> file: ImageA.mnc
> image: unsigned short 0 to 4095
> image dimensions: yspace zspace xspace
> dimension name length step start
> -------------- ------ ---- -----
> yspace 128 -1 13.7688
> zspace 192 -1.04167 115.005
> xspace 88 -1.04167 38.0225
>
>
>
>
>
>
>
>
>
> $ mincreshape +ydirection -unsigned -short ImageA.mnc ImageB.mnc
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> Copying chunks:................................................................................................................................Done.
>
> $ mincinfo ImageB.mncfile: ImageB.mncimage: unsigned short 0 to 65535image dimensions: yspace zspace xspace dimension name length step start -------------- ------ ---- ----- yspace 128 -1 13.7688 zspace 192 -1.04167 115.005
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> xspace 88 -1.04167 38.0225
>
>
>
>
>
>
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 17 Mar 2015 23:10:12 +0100
> From: Alex Zijdenbos <zijdenbos at gmail.com>
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> Subject: Re: [MINC-users] mincreshape +direction
> Message-ID:
> <CABEEk156aeULZSNvuaUkJ-1XwAMwFn3LarFOXMtA40Rsgimm-A at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Jessie,
>
> Having bitten by this (rather counter-intuitive I'll admit) behaviour more
> than once mysefl, I can answer your question: mincreshape's +/-direction
> options only work on image dimensions, which are the two fastest-varying
> dimensions. In your case, yspace is not an "image dimension" as it is the
> slowest-varyinhg dimension.
>
> You'll need to convert yspace to be an image dimension first - check the
> mincreshape man page and examples for how exactly to do that.
>
> -- Alex
>
> On Tue, Mar 17, 2015 at 10:22 PM, ting guo <jessieguo80 at hotmail.com> wrote:
>
> > Dear Minc Users,
> > I was trying to use mincreshape to flip a image to give positive yspace,
> > but it didn't work. The following are what I did and what I got as results.
> > As you can see, the image remains unchanged. Am I missing certain important
> > options? How can I flip the image and have positive yspace? I would really
> > appreciate your suggestions.
> > Thank you very much!
> > Jessie
> > $ mincinfo ImageA.mnc
> >
> >
> >
> >
> >
> >
> >
> > file: ImageA.mnc
> > image: unsigned short 0 to 4095
> > image dimensions: yspace zspace xspace
> > dimension name length step start
> > -------------- ------ ---- -----
> > yspace 128 -1 13.7688
> > zspace 192 -1.04167 115.005
> > xspace 88 -1.04167 38.0225
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > $ mincreshape +ydirection -unsigned -short ImageA.mnc ImageB.mnc
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > Copying
> > chunks:................................................................................................................................Done.
> >
> > $ mincinfo ImageB.mncfile: ImageB.mncimage: unsigned short 0 to 65535image
> > dimensions: yspace zspace xspace dimension name length
> > step start -------------- ------ ----
> > ----- yspace 128 -1 13.7688 zspace
> > 192 -1.04167 115.005
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > xspace 88 -1.04167 38.0225
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> >
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 17 Mar 2015 22:35:44 +0000
> From: Oury Monchi <Oury.Monchi at ucalgary.ca>
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> Cc: "G. Bruce Pike" <bruce.pike at ucalgary.ca>
> Subject: [MINC-users] IT position in neuroimaging at University of
> Calgary
> Message-ID: <D12E085E.1B1F5%oury.monchi at ucalgary.ca>
> Content-Type: text/plain; charset="Windows-1252"
>
> Dear all,
>
> I would like to bring to your attention to the following Neuroimaging IT support position to work with Dr. Bruce Pike and myself at the University of Calgary:
>
> http://careers.ucalgary.ca/jobs/3484069-neuroimaging-it-system-support-radiology-cumming-school-of-medicine
>
> Best,
> Oury.
>
> Oury Monchi, PhD
>
> Professor and Tourmaline Chair in Parkinson?s Disease,
>
> Research Director of the Movement Disorders Program,
>
> Director of Clinical Research,
>
> Department of Clinical Neurosciences,
>
> Hotchkiss Brain Institute,
>
> Cumming School of Medicine, University of Calgary.
> Tel: 403-2208048
> http://pcanlab.ca/
>
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 18 Mar 2015 00:04:41 -0400
> From: "Vladimir S. FONOV" <vladimir.fonov at gmail.com>
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> Subject: Re: [MINC-users] mincreshape +direction
> Message-ID:
> <CAMCwi7OL9YmY53dcbfxWc6gfSn2tv2JA8-+_H2v=FgGVTo55SQ at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> to convert to the "image dimension" use -dimsize yspace=-1
>
>
> On Tue, Mar 17, 2015 at 6:10 PM, Alex Zijdenbos <zijdenbos at gmail.com> wrote:
>
> > Hi Jessie,
> >
> > Having bitten by this (rather counter-intuitive I'll admit) behaviour more
> > than once mysefl, I can answer your question: mincreshape's +/-direction
> > options only work on image dimensions, which are the two fastest-varying
> > dimensions. In your case, yspace is not an "image dimension" as it is the
> > slowest-varyinhg dimension.
> >
> > You'll need to convert yspace to be an image dimension first - check the
> > mincreshape man page and examples for how exactly to do that.
> >
> > -- Alex
> >
> > On Tue, Mar 17, 2015 at 10:22 PM, ting guo <jessieguo80 at hotmail.com>
> > wrote:
> >
> > > Dear Minc Users,
> > > I was trying to use mincreshape to flip a image to give positive yspace,
> > > but it didn't work. The following are what I did and what I got as
> > results.
> > > As you can see, the image remains unchanged. Am I missing certain
> > important
> > > options? How can I flip the image and have positive yspace? I would
> > really
> > > appreciate your suggestions.
> > > Thank you very much!
> > > Jessie
> > > $ mincinfo ImageA.mnc
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > file: ImageA.mnc
> > > image: unsigned short 0 to 4095
> > > image dimensions: yspace zspace xspace
> > > dimension name length step start
> > > -------------- ------ ---- -----
> > > yspace 128 -1 13.7688
> > > zspace 192 -1.04167 115.005
> > > xspace 88 -1.04167 38.0225
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > $ mincreshape +ydirection -unsigned -short ImageA.mnc ImageB.mnc
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > Copying
> > >
> > chunks:................................................................................................................................Done.
> > >
> > > $ mincinfo ImageB.mncfile: ImageB.mncimage: unsigned short 0 to
> > 65535image
> > > dimensions: yspace zspace xspace dimension name length
> > > step start -------------- ------ ----
> > > ----- yspace 128 -1 13.7688
> > zspace
> > > 192 -1.04167 115.005
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > xspace 88 -1.04167 38.0225
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > 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
>
>
> ------------------------------
>
> _______________________________________________
> MINC-users mailing list
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>
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