From minc-users@bic.mni.mcgill.ca Mon Jul 21 17:34:54 2003 From: minc-users@bic.mni.mcgill.ca (Christophe Grova) Date: Mon, 21 Jul 2003 10:34:54 -0600 Subject: [MINC-users] Question concerning minctoraw References: <005901c32599$6ecf28c0$6402a8c0@cgrova> Message-ID: <000f01c34fa6$04027060$e136d884@cgrova> Hello everybody, I try to use minctoraw to convert SPECT data in minc. My data are stored either in float or in short and I would like to convert them in minc so that the value stored in the buffer remain exactly the same when they are read from a the minc file. In other words, I have some problems using the options concerning the intensity range (I tried 'real_range', 'orange', without success....), and I would like that using for instance the viewer Display, the same intensity value appears after 'Vx' and 'Vl' .... is there a simple way to do that ? Thanks in advance, Christophe *************************** Christophe Grova, PhD PostDoc - EEG department Montreal Neurological Institute, McGill University 3801 University Street, Montreal, Quebec, Canada, H3A 2B4 email : christophe.grova@mail.mcgill.ca tel : (514) 398 2184 fax : (514) 398 8106 web: http://idm.univ-rennes1.fr/users/grova *************************** From Ona Wu Mon Jul 21 16:26:52 2003 From: Ona Wu (Ona Wu) Date: Mon, 21 Jul 2003 17:26:52 +0200 (CEST) Subject: [MINC-users] Question concerning minctoraw In-Reply-To: <000f01c34fa6$04027060$e136d884@cgrova> References: <005901c32599$6ecf28c0$6402a8c0@cgrova> <000f01c34fa6$04027060$e136d884@cgrova> Message-ID: Hi Christophe, I've also had similar problems. The trick seems to be to properly save the raw files in MINC in the first place. What works for me is to find the maximum and minimum of your raw files, then call rawtominc with -real_range and -range options set accordingly. Then when I want the raw file back, I call minctoraw with the -normalize option. Please let me know if this works for you as well. Ona On Mon, 21 Jul 2003, Christophe Grova wrote: > Hello everybody, > > I try to use minctoraw to convert SPECT data in minc. > My data are stored either in float or in short and I would like to convert > them in minc so that the value stored in the buffer remain exactly the same > when they are read from a the minc file. > > In other words, I have some problems using the options concerning the > intensity range (I tried 'real_range', 'orange', without success....), and I > would like that using for instance the viewer Display, the same intensity > value appears after 'Vx' and 'Vl' .... is there a simple way to do that ? > > Thanks in advance, > > Christophe > > *************************** > Christophe Grova, PhD > PostDoc - EEG department > Montreal Neurological Institute, McGill University > 3801 University Street, Montreal, Quebec, Canada, H3A 2B4 > email : christophe.grova@mail.mcgill.ca > tel : (514) 398 2184 > fax : (514) 398 8106 > web: http://idm.univ-rennes1.fr/users/grova > *************************** > > > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From minc-users@bic.mni.mcgill.ca Thu Jul 24 18:34:59 2003 From: minc-users@bic.mni.mcgill.ca (Joost Janssen) Date: Thu, 24 Jul 2003 19:34:59 +0200 (METDST) Subject: [MINC-users] (no subject) Message-ID: Hi, i used mincreshape to select seperate parts from my original file: mincreshape -dimrange yspace=1,1 original.mnc new1.mnc mincreshape -dimrange yspace=2,1 original.mnc new2.mnc etc. how can i put together the 'new*.mnc' files to create the original file? -joost From minc-users@bic.mni.mcgill.ca Fri Jul 25 01:25:43 2003 From: minc-users@bic.mni.mcgill.ca (Andrew Janke) Date: Fri, 25 Jul 2003 10:25:43 +1000 Subject: [MINC-users] (no subject) In-Reply-To: References: Message-ID: On Thu, 24 Jul 2003, Joost Janssen wrote: > i used mincreshape to select seperate parts from my original file: > > mincreshape -dimrange yspace=1,1 original.mnc new1.mnc > mincreshape -dimrange yspace=2,1 original.mnc new2.mnc > > etc. > > how can i put together the 'new*.mnc' files to create the original file? mincconcat will make a pretty intelligent guess as to how to put them back together. 'minconcat -help' or 'man mincconcat' should be able to assist you here. -- Andrew Janke ( rotor@cmr.uq.edu.au || www.cmr.uq.edu.au/~rotor ) Australia->University of Queensland->Centre for Magnetic Resonance W: +61 7 3365 4100 || H: +61 7 3800 4042 || M: +61 4 2138 8581 From minc-users@bic.mni.mcgill.ca Mon Jul 28 11:10:45 2003 From: minc-users@bic.mni.mcgill.ca (Joost Janssen) Date: Mon, 28 Jul 2003 12:10:45 +0200 (METDST) Subject: [MINC-users] mincconcat In-Reply-To: <200307251601.h6PG16F953490@shadow.bic.mni.mcgill.ca> Message-ID: Thanks Andrew, when i use mincconcat on 2 files that look like: 1) image: unsigned float 0 to 3 image dimensions: zspace yspace xspace dimension name length step start -------------- ------ ---- ----- zspace 181 1 -0 yspace 1 1.6 20.8 xspace 193 1 -0 2) image: unsigned float 0 to 3 image dimensions: zspace yspace xspace dimension name length step start -------------- ------ ---- ----- zspace 181 1 -0 yspace 1 1.6 22.4 xspace 193 1 -0 and my goal is to concatenate them along the y-axis, i WOULD LIKE to see the following file: 1) + 2) dimension name length step start -------------- ------ ---- ----- zspace 181 1 -0 yspace 2 1.6 20.8 xspace 193 1 -0 how do i do this? when i use mincconcat now on these files (mincconcat infile infile outfile nocheck_dimensions) i get: dimension name length step start -------------- ------ ---- ----- zspace 362 0.498615 0 yspace 1 1.6 20.8 xspace 193 1 -0 it's concatenating along the z-axis. specifying the y-axis (-concat_dimension yspace) gives an error message. thanks, -joost ********************************** Joost Janssen Utrecht University Medical Center Department of psychiatry Structural imaging group A01.126 Heidelberglaan 100 3584 GX Utrecht The Netherlands #work:(0031)-30-2501783 e-mail:jjanssen@azu.nl www.smri.nl ********************************** > Send MINC-users mailing list submissions to > minc-users@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@bic.mni.mcgill.ca > > You can reach the person managing the list at > minc-users-admin@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. (no subject) (Joost Janssen) > 2. Re: (no subject) (Andrew Janke) > > --__--__-- > > Message: 1 > Date: Thu, 24 Jul 2003 19:34:59 +0200 (METDST) > From: Joost Janssen > To: minc-users@bic.mni.mcgill.ca > Subject: [MINC-users] (no subject) > Reply-To: minc-users@bic.mni.mcgill.ca > > Hi, > > i used mincreshape to select seperate parts from my original file: > > mincreshape -dimrange yspace=1,1 original.mnc new1.mnc > mincreshape -dimrange yspace=2,1 original.mnc new2.mnc > > etc. > > how can i put together the 'new*.mnc' files to create the original file? > > -joost > > > --__--__-- > > Message: 2 > Date: Fri, 25 Jul 2003 10:25:43 +1000 > From: Andrew Janke > To: minc-users@bic.mni.mcgill.ca > Subject: Re: [MINC-users] (no subject) > Reply-To: minc-users@bic.mni.mcgill.ca > > On Thu, 24 Jul 2003, Joost Janssen wrote: > > > i used mincreshape to select seperate parts from my original file: > > > > mincreshape -dimrange yspace=1,1 original.mnc new1.mnc > > mincreshape -dimrange yspace=2,1 original.mnc new2.mnc > > > > etc. > > > > how can i put together the 'new*.mnc' files to create the original file? > > mincconcat will make a pretty intelligent guess as to how to put them back > together. > > 'minconcat -help' or 'man mincconcat' should be able to assist you here. > > > -- > Andrew Janke ( rotor@cmr.uq.edu.au || www.cmr.uq.edu.au/~rotor ) > Australia->University of Queensland->Centre for Magnetic Resonance > W: +61 7 3365 4100 || H: +61 7 3800 4042 || M: +61 4 2138 8581 > > > --__--__-- > > _______________________________________________ > MINC-users mailing list > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > End of MINC-users Digest > From minc-users@bic.mni.mcgill.ca Wed Jul 30 01:45:20 2003 From: minc-users@bic.mni.mcgill.ca (Peter NEELIN) Date: Tue, 29 Jul 2003 20:45:20 -0400 Subject: [MINC-users] mincconcat In-Reply-To: Message-ID: On Mon, 28 Jul 2003, Joost Janssen wrote: > it's concatenating along the z-axis. specifying the y-axis > (-concat_dimension yspace) gives an error message. mincconcat will concatenate along the slowest-varying axis by default. Unfortunately, it will not concatenate along "image" dimensions (the fastest-varying 2, or 3 if it is a vector file). The solution (a bit ugly) is to reorder the dimensions using either mincresample or mincreshape so that the order is yzx and then use mincconcat. To get the desired order back you would need to then do a mincresample again: mincresample -nearest -coronal new1.mnc new1_cor.mnc mincresample -nearest -coronal new2.mnc new2_cor.mnc mincconcat new1_cor.mnc new2_cor.mnc new_cor.mnc mincresample -nearest -transverse new_cor.mnc new.mnc Ugly, but it should work (although I have not tried it, so I've probably forgotten something). Peter ---- Peter Neelin (neelin@bic.mni.mcgill.ca)