[MINC-users] mincnlm

[Louis Dieumegarde]

It works! Thank you.

Louis Dieumegarde




On 2018-05-17, 12:00 PM, "minc-users-bounces at bic.mni.mcgill.ca on behalf of minc-users-request at bic.mni.mcgill.ca" <minc-users-bounces at bic.mni.mcgill.ca on behalf of minc-users-request at bic.mni.mcgill.ca> wrote:

    Send MINC-users mailing list submissions to
    	minc-users at bic.mni.mcgill.ca
    
    To subscribe or unsubscribe via the World Wide Web, visit
    	http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
    or, via email, send a message with subject or body 'help' to
    	minc-users-request at bic.mni.mcgill.ca
    
    You can reach the person managing the list at
    	minc-users-owner at bic.mni.mcgill.ca
    
    When replying, please edit your Subject line so it is more specific
    than "Re: Contents of MINC-users digest..."
    
    
    Today's Topics:
    
       1. mincnlm (Louis Dieumegarde)
       2. Re: mincnlm (Vladimir S. FONOV)
    
    
    ----------------------------------------------------------------------
    
    Message: 1
    Date: Wed, 16 May 2018 18:01:25 +0000
    From: Louis Dieumegarde <louis.dieumegarde at crulrg.ulaval.ca>
    To: "minc-users at bic.mni.mcgill.ca" <minc-users at bic.mni.mcgill.ca>
    Subject: [MINC-users] mincnlm
    Message-ID: <19E0E680-E0BC-4BA7-B3FC-54E0D5CE5ED0 at ulaval.ca>
    Content-Type: text/plain; charset="utf-8"
    
       Bonjour,
    
    
       We have a problem when using the mincnlm tool with mri_convert. Once
       the denoised minc file is convert to MGZ, we have an intensity range of
       -32768 to 32767.
    
    
       I tried the no_scale flag without success. I tried the -odt flag, the
       range become 0-255, but there is still the wide disparity between some
       voxels in the lower vs upper range.
    
    
       The denoised minc is ok when we use register or mincstats. Even when we
       open directly the denoised minc in freeview, the problem appears.
    
    
       Is there a conversion in the denoised tool that is not compatible with
       freesurfer?
    
    
       Thank you.
    
    
       Louis Dieumegarde
    
       Data scientist / Professionnel de recherche
    
       Laboratoire Medics
    
    
    ------------------------------
    
    Message: 2
    Date: Wed, 16 May 2018 14:03:52 -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] mincnlm
    Message-ID:
    	<CAMCwi7NprkytegKbFRa2eKYaMwJgV5tCDQJeJkeTZ5twhhCtdA at mail.gmail.com>
    Content-Type: text/plain; charset="UTF-8"
    
    Hello,
    
    Try converting it to float before running minnlm (i.e mincreshape -float
    <in> <out> )
    
    On 16 May 2018 at 14:01, Louis Dieumegarde <
    louis.dieumegarde at crulrg.ulaval.ca> wrote:
    
    >    Bonjour,
    >
    >
    >    We have a problem when using the mincnlm tool with mri_convert. Once
    >    the denoised minc file is convert to MGZ, we have an intensity range of
    >    -32768 to 32767.
    >
    >
    >    I tried the no_scale flag without success. I tried the -odt flag, the
    >    range become 0-255, but there is still the wide disparity between some
    >    voxels in the lower vs upper range.
    >
    >
    >    The denoised minc is ok when we use register or mincstats. Even when we
    >    open directly the denoised minc in freeview, the problem appears.
    >
    >
    >    Is there a conversion in the denoised tool that is not compatible with
    >    freesurfer?
    >
    >
    >    Thank you.
    >
    >
    >    Louis Dieumegarde
    >
    >    Data scientist / Professionnel de recherche
    >
    >    Laboratoire Medics
    > _______________________________________________
    > 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
    
    
    End of MINC-users Digest, Vol 151, Issue 1
    ******************************************