From minc-users@bic.mni.mcgill.ca Thu Sep 4 01:11:15 2003 From: minc-users@bic.mni.mcgill.ca (Andrew Janke) Date: Thu, 4 Sep 2003 10:11:15 +1000 Subject: [MINC-users] Re: [BIC-users] minc basics Message-ID: On Tue, 2 Sep 2003, Natasa Kovacevic wrote: > Given a minc file with who-knows-which order of spatial dimensions and > who-knows-what start and steps , I would like to produce a minc file > that contains the same data with the same coordinate system, but: > dimension ordering is z,y,x (from slowest to fastest) and > all steps have positive directions > > I thought that something like : > > mincreshape +direction -dimorder zspace,yspace,xspace IN.mnc OUT.mnc > > would do the trick, but it doesn't (dimension order is o.k, but if some > step in IN.mnc is negative, it is the same in OUT.mnc) This would seem sensible, however there is a slight trick to this, 'man mincreshape' goes into this in more detail but suffice to say here is an all encompasing command that I use that should work in your case: $ mincreshape +direction -dimorder zspace,yspace,xspace \ -dimsize xspace=-1 -dimsize yspace=-1 -dimsize zspace=-1 \ infile.mnc outfile.mnc -- 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 Thu Sep 25 19:17:11 2003 From: minc-users@bic.mni.mcgill.ca (Andre MATOS) Date: Thu, 25 Sep 2003 14:17:11 -0400 (EDT) Subject: [MINC-users] Differences between mincstats and volume_stats Message-ID: I was comparing the results from mincstats and the volume_stats and I found some different values, specially in Median. The mincstats was run into a Mac and the volume_stats into Linux. Below are both: mincstats sanca6_MTe2.mnc.gz -mask sanca6_2003_09_22_bayes1.mnc.gz -mask_range 4,4 -all File: sanca6_MTe2.mnc.gz Mask file: sanca6_2003_09_22_bayes1.mnc.gz Total voxels: 3276800 # voxels: 158878 % of total: 4.848571777 Volume (mm3): 454553.6041 Min: -0.02046138374 Max: 61.16808724 Sum: 5805114.165 Sum^2: 213541256.4 Mean: 36.53818757 Variance: 9.018965791 Stddev: 3.003159302 CoM_voxel(z,y,x): 28.03302643 142.6857334 128.9361516 CoM_real(x,y,z): -1.402491803 40.19036803 6.234843781 Histogram: (null) Total voxels: 3276800 # voxels: 158878 % of total: 4.848571777 Median: 241.5912838 Majority: 37.16630936 BiModalT: 61.20598221 PctT [ 0%]: 0 Entropy : 6.305040492 Bus error -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- volume_stats sanca6_MTe2.mnc.gz -mask sanca6_2003_09_22_bayes1.mnc.gz -maskrange 4 4 -all File: sanca6_MTe2.mnc.gz Mask: sanca6_2003_09_22_bayes1.mnc.gz Mask extrema: [4, 4] # voxels: 158878 % of total: 4.84857 Volume (mm3): 454554 Min: -0.0271893 Max: 61.1572 Sum: 5.8051e+06 Sum2: 2.1354e+08 Mean: 36.5381 Variance: 9.01985 Stddev: 3.00331 Median: 36.8731 Majority: 37.1616 BiModalT: 35.8467 PctT (-1.79769e+308): -0.0346599 61.1647 Entropy: 7.33663 CoM_voxel: zspace:28.033 yspace:142.686 xspace:128.936 CoM_world: zspace:6.23486 yspace:40.1904 xspace:-1.40249 Is anyone tryed to compile the volume_stats (N3 package) into a Mac OS X and also know which program (mincstats or volume_stats) is right? -- Andre Matos amatos@mrs.mni.mcgill.ca ------------- B BTW, has anyone tested using mincstats as a drop-in replacement - can one just symlink volume_stats to mincstats and scripts work properly (producing the same output)? Peter ---- Peter Neelin (neelin@bic.mni.mcgill.ca) From minc-users@bic.mni.mcgill.ca Sat Sep 27 05:09:57 2003 From: minc-users@bic.mni.mcgill.ca (Andrew Janke) Date: Sat, 27 Sep 2003 14:09:57 +1000 Subject: [MINC-users] Differences between mincstats and volume_stats In-Reply-To: References: Message-ID: On Thu, 25 Sep 2003, Andre MATOS wrote: > I was comparing the results from mincstats and the volume_stats and I > found some different values, specially in Median. The mincstats was > run into a Mac and the volume_stats into Linux. Below are both: > > mincstats sanca6_MTe2.mnc.gz -mask sanca6_2003_09_22_bayes1.mnc.gz > -mask_range 4,4 -all > ... > > Bus error This error (I think) is a memory allocation problem that has been fixed in later releases. Which version of minc are you running? > Is anyone tryed to compile the volume_stats (N3 package) into a Mac OS X > and also know which program (mincstats or volume_stats) is right? The answer is: Both are right. However the two have a differing opinion of how a histogram bin should be defined and also how many bins there should be in a histogram. 'man mincstats' will tell you how you can get mincstats to more closely resemble volume_stats. The base statistics should not differ (apart from via rounding errors) but the histogram stats (of which median is one) are definitely going to differ if you use the default options. As for using mincstats instead of volume_stats in the mni_autoreg package, in 99% of cases there will be identical functionality. N3 may well have differences though as the authour of N3 is also the authour of volume_stats... -- 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 Sat Sep 27 18:39:34 2003 From: minc-users@bic.mni.mcgill.ca (Alex ZIJDENBOS) Date: Sat, 27 Sep 2003 13:39:34 -0400 Subject: [MINC-users] Differences between mincstats and volume_stats In-Reply-To: References: Message-ID: <20030927173933.GA888522@shadow.bic.mni.mcgill.ca> On Sat, Sep 27, 2003 at 02:09:57PM +1000, Andrew Janke wrote: > As for using mincstats instead of volume_stats in the mni_autoreg package, in > 99% of cases there will be identical functionality. N3 may well have > differences though as the authour of N3 is also the authour of volume_stats... Actually, minor correction here: John Sled wrote N3, I wrote volume_stats :) -- A From minc-users@bic.mni.mcgill.ca Sat Sep 27 22:49:24 2003 From: minc-users@bic.mni.mcgill.ca (Andre MATOS) Date: Sat, 27 Sep 2003 17:49:24 -0400 (EDT) Subject: [MINC-users] Differences between mincstats and volume_stats In-Reply-To: <20030927173933.GA888522@shadow.bic.mni.mcgill.ca> Message-ID: Hi Alex, I'm trying to compile the volume_stats (N3 package) but I got some errors. I tried into Linux RedHat 9 and also in MacOS X, but both showed the same errors. I tooks a quick look and it seens that just volume_stats was not compilied. Do you have any suggestion? Thanks! Andre Matos amatos@mrs.mni.mcgill.ca On Sat, 27 Sep 2003, Alex ZIJDENBOS wrote: > On Sat, Sep 27, 2003 at 02:09:57PM +1000, Andrew Janke wrote: > > As for using mincstats instead of volume_stats in the mni_autoreg package, in > > 99% of cases there will be identical functionality. N3 may well have > > differences though as the authour of N3 is also the authour of volume_stats... > > Actually, minor correction here: John Sled wrote N3, I wrote > volume_stats :) > > -- A > _______________________________________________ > MINC-users@bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > -- Andre Matos amatos@mrs.mni.mcgill.ca From minc-users@bic.mni.mcgill.ca Sat Sep 27 22:56:50 2003 From: minc-users@bic.mni.mcgill.ca (Andre MATOS) Date: Sat, 27 Sep 2003 17:56:50 -0400 (EDT) Subject: [MINC-users] Differences between mincstats and volume_stats In-Reply-To: Message-ID: Hi Andrew, On Sat, 27 Sep 2003, Andrew Janke wrote: > On Thu, 25 Sep 2003, Andre MATOS wrote: > > > I was comparing the results from mincstats and the volume_stats and I > > found some different values, specially in Median. The mincstats was > > run into a Mac and the volume_stats into Linux. Below are both: > > > > mincstats sanca6_MTe2.mnc.gz -mask sanca6_2003_09_22_bayes1.mnc.gz > > -mask_range 4,4 -all > > ... > > > > Bus error > > This error (I think) is a memory allocation problem that has been fixed in later > releases. Which version of minc are you running? I am using the version 1.1. I tried to recompiled into MacOS X but I got the "Bus error" again. > > > Is anyone tryed to compile the volume_stats (N3 package) into a Mac OS X > > and also know which program (mincstats or volume_stats) is right? > > The answer is: Both are right. However the two have a differing opinion of how > a histogram bin should be defined and also how many bins there should be in a > histogram. > > 'man mincstats' will tell you how you can get mincstats to more closely > resemble volume_stats. The base statistics should not differ (apart from via > rounding errors) but the histogram stats (of which median is one) are definitely > going to differ if you use the default options. > > As for using mincstats instead of volume_stats in the mni_autoreg package, in > 99% of cases there will be identical functionality. N3 may well have > differences though as the authour of N3 is also the authour of volume_stats... > Do you know how can I make mincstats to show the "same" value, especially in "-median", as the volume_stats? Thanks. -- Andre Matos amatos@mrs.mni.mcgill.ca From minc-users@bic.mni.mcgill.ca Mon Sep 29 15:15:46 2003 From: minc-users@bic.mni.mcgill.ca (Jason Lerch) Date: Mon, 29 Sep 2003 10:15:46 -0400 Subject: [MINC-users] Differences between mincstats and volume_stats In-Reply-To: References: Message-ID: <1064844946.23732.11.camel@dennis.bic.mni.mcgill.ca> Greetings, I'm afraid that the statement "I got some errors" isn't all that enlightening when trying to help you debug your problem. Could you maybe send some more info, such as what the error was that you got, what compiler you used, what version of N3 you were compiling, etc. Jason On Sat, 2003-09-27 at 17:49, Andre MATOS wrote: > Hi Alex, > > I'm trying to compile the volume_stats (N3 package) but I got some errors. > I tried into Linux RedHat 9 and also in MacOS X, but both showed the same > errors. I tooks a quick look and it seens that just volume_stats was not > compilied. Do you have any suggestion? > > Thanks! > > Andre Matos > amatos@mrs.mni.mcgill.ca > > > On Sat, 27 Sep 2003, Alex ZIJDENBOS wrote: > > > On Sat, Sep 27, 2003 at 02:09:57PM +1000, Andrew Janke wrote: > > > As for using mincstats instead of volume_stats in the mni_autoreg package, in > > > 99% of cases there will be identical functionality. N3 may well have > > > differences though as the authour of N3 is also the authour of volume_stats... > > > > Actually, minor correction here: John Sled wrote N3, I wrote > > volume_stats :) > > > > -- A > > _______________________________________________ > > MINC-users@bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > From minc-users@bic.mni.mcgill.ca Mon Sep 29 17:53:21 2003 From: minc-users@bic.mni.mcgill.ca (Yoshitaka KUMAKURA) Date: Mon, 29 Sep 2003 12:53:21 -0400 Subject: [MINC-users] GE Advance's Dicom 4D PET data In-Reply-To: <1064844946.23732.11.camel@dennis.bic.mni.mcgill.ca> Message-ID: Hello minc users, What is the correct procedure to get GE Advance's Dicom 4D PET data converted to minc? Best regards, Yoshi (for Tokyo University) kumakura@bic.mni.mcgill.ca From minc-users@bic.mni.mcgill.ca Mon Sep 29 16:01:38 2003 From: minc-users@bic.mni.mcgill.ca (Shapoor) Date: Mon, 29 Sep 2003 11:01:38 -0400 Subject: [MINC-users] Shapoor from Dr. Bushnell's lab Message-ID: <000f01c3869a$951fca40$c22bd884@medserv.mcgill.ca> This is a multi-part message in MIME format. ------=_NextPart_000_0010_01C38679.0E0E2A40 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Hi, I have files that are in dicom format, I was wondering how can I transfer them into minc format? Thank you Shapoor ------=_NextPart_000_0010_01C38679.0E0E2A40 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hi,

 

I have files that are in dicom format, I was = wondering how can I transfer them into minc format?

 

Thank you

Shapoor

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