From louis.dieumegarde at crulrg.ulaval.ca Wed May 16 14:01:25 2018 From: louis.dieumegarde at crulrg.ulaval.ca (Louis Dieumegarde) Date: Wed, 16 May 2018 18:01:25 +0000 Subject: [MINC-users] mincnlm Message-ID: <19E0E680-E0BC-4BA7-B3FC-54E0D5CE5ED0@ulaval.ca> 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 From vladimir.fonov at gmail.com Wed May 16 14:03:52 2018 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Wed, 16 May 2018 14:03:52 -0400 Subject: [MINC-users] mincnlm In-Reply-To: <19E0E680-E0BC-4BA7-B3FC-54E0D5CE5ED0@ulaval.ca> References: <19E0E680-E0BC-4BA7-B3FC-54E0D5CE5ED0@ulaval.ca> Message-ID: Hello, Try converting it to float before running minnlm (i.e mincreshape -float ) 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 fonov gmail com From louis.dieumegarde at crulrg.ulaval.ca Tue May 22 09:43:00 2018 From: louis.dieumegarde at crulrg.ulaval.ca (Louis Dieumegarde) Date: Tue, 22 May 2018 13:43:00 +0000 Subject: [MINC-users] mincnlm Message-ID: 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" 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 To: "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" To: MINC users mailing list Subject: Re: [MINC-users] mincnlm Message-ID: Content-Type: text/plain; charset="UTF-8" Hello, Try converting it to float before running minnlm (i.e mincreshape -float ) 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 fonov gmail 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 ******************************************