From gavin.elias at mail.utoronto.ca Wed Oct 11 19:29:10 2017 From: gavin.elias at mail.utoronto.ca (Gavin Elias) Date: Wed, 11 Oct 2017 23:29:10 +0000 Subject: [MINC-users] DICOM to MINC conversion error Message-ID: Hi, I have been converting dicom files to minc using the dcm2mnc command. I preprocessed these dicom files in Horos on my laptop, where I decompressed, anonymized, and then exported them. For certain files, however, the dcm2mnc command is failing and I am receiving the following error when I run it: 'ERROR: Age units (048Y) unknown.' I am able to convert these dicom files to nifti format with no issue and convert from nifti to dicom fine. I have tried processing the same dicom files in other versions of Horos and have encountered the same error during dcm2mnc. A colleague of mine has been able to preprocess the same dicom files in Horos on his own laptop and was able to subsequently convert them to minc with no problem. I am not sure what is causing the dcm2mnc conversion to fail. Any help would be much appreciated. Thanks, Gavin From a.janke at gmail.com Wed Oct 11 19:44:04 2017 From: a.janke at gmail.com (Andrew Janke) Date: Thu, 12 Oct 2017 09:44:04 +1000 Subject: [MINC-users] DICOM to MINC conversion error In-Reply-To: References: Message-ID: Hi Gavin, This looks like a bug in dcm2mnc in which it fails to recognise the Y as years on the end of the age. There will need to be a patch for this but in the meantime if age isn't that important to you, you could delete the element in the input DICOM files? $ dcmodify -ea "(0010,1010)" I recall that 0010,1010 is the tag for age. (if not, use dcmdump to find it). And then run the conversion again? a On 12 October 2017 at 09:29, Gavin Elias wrote: > Hi, > > I have been converting dicom files to minc using the dcm2mnc command. I preprocessed these dicom files in Horos on my laptop, where I decompressed, anonymized, and then exported them. For certain files, however, the dcm2mnc command is failing and I am receiving the following error when I run it: 'ERROR: Age units (048Y) unknown.' > > I am able to convert these dicom files to nifti format with no issue and convert from nifti to dicom fine. I have tried processing the same dicom files in other versions of Horos and have encountered the same error during dcm2mnc. A colleague of mine has been able to preprocess the same dicom files in Horos on his own laptop and was able to subsequently convert them to minc with no problem. I am not sure what is causing the dcm2mnc conversion to fail. > > Any help would be much appreciated. > > Thanks, > > Gavin > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From bert at phalarope.com Wed Oct 11 19:51:21 2017 From: bert at phalarope.com (Robert D. Vincent) Date: Wed, 11 Oct 2017 19:51:21 -0400 Subject: [MINC-users] DICOM to MINC conversion error In-Reply-To: References: Message-ID: Hi Gavin, That's an old bug in dcm2mnc, it was fixed quite a while back. You can get the updated version as part of the latest minc toolkit distribution: https://bic-mni.github.io/ -bert On Wed, Oct 11, 2017 at 7:29 PM, Gavin Elias wrote: > Hi, > > I have been converting dicom files to minc using the dcm2mnc command. I > preprocessed these dicom files in Horos on my laptop, where I decompressed, > anonymized, and then exported them. For certain files, however, the > dcm2mnc command is failing and I am receiving the following error when I > run it: 'ERROR: Age units (048Y) unknown.' > > I am able to convert these dicom files to nifti format with no issue and > convert from nifti to dicom fine. I have tried processing the same dicom > files in other versions of Horos and have encountered the same error during > dcm2mnc. A colleague of mine has been able to preprocess the same dicom > files in Horos on his own laptop and was able to subsequently convert them > to minc with no problem. I am not sure what is causing the dcm2mnc > conversion to fail. > > Any help would be much appreciated. > > Thanks, > > Gavin > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From gavin.elias at mail.utoronto.ca Mon Oct 16 14:18:58 2017 From: gavin.elias at mail.utoronto.ca (Gavin Elias) Date: Mon, 16 Oct 2017 18:18:58 +0000 Subject: [MINC-users] MINC-users Digest, Vol 145, Issue 1 In-Reply-To: References: Message-ID: <36D106D9-6A6F-40A4-9159-5208D62CDB93@mail.utoronto.ca> Thanks for your responses! I found that the command '$ dcmodify -ea "(0010,1010)" ? did the trick and allowed me to subsequently run dcm2mnc. Gavin On 2017-10-12, 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. DICOM to MINC conversion error (Gavin Elias) > 2. Re: DICOM to MINC conversion error (Andrew Janke) > 3. Re: DICOM to MINC conversion error (Robert D. Vincent) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Wed, 11 Oct 2017 23:29:10 +0000 >From: Gavin Elias >To: "minc-users at bic.mni.mcgill.ca" >Subject: [MINC-users] DICOM to MINC conversion error >Message-ID: >Content-Type: text/plain; charset="us-ascii" > >Hi, > >I have been converting dicom files to minc using the dcm2mnc command. I preprocessed these dicom files in Horos on my laptop, where I decompressed, anonymized, and then exported them. For certain files, however, the dcm2mnc command is failing and I am receiving the following error when I run it: 'ERROR: Age units (048Y) unknown.' > >I am able to convert these dicom files to nifti format with no issue and convert from nifti to dicom fine. I have tried processing the same dicom files in other versions of Horos and have encountered the same error during dcm2mnc. A colleague of mine has been able to preprocess the same dicom files in Horos on his own laptop and was able to subsequently convert them to minc with no problem. I am not sure what is causing the dcm2mnc conversion to fail. > >Any help would be much appreciated. > >Thanks, > >Gavin > >------------------------------ > >Message: 2 >Date: Thu, 12 Oct 2017 09:44:04 +1000 >From: Andrew Janke >To: MINC users mailing list >Subject: Re: [MINC-users] DICOM to MINC conversion error >Message-ID: > >Content-Type: text/plain; charset="UTF-8" > >Hi Gavin, > >This looks like a bug in dcm2mnc in which it fails to recognise the Y >as years on the end of the age. There will need to be a patch for >this but in the meantime if age isn't that important to you, you could >delete the element in the input DICOM files? > > $ dcmodify -ea "(0010,1010)" > >I recall that 0010,1010 is the tag for age. (if not, use dcmdump to find it). > >And then run the conversion again? > > >a > > >On 12 October 2017 at 09:29, Gavin Elias wrote: >> Hi, >> >> I have been converting dicom files to minc using the dcm2mnc command. I preprocessed these dicom files in Horos on my laptop, where I decompressed, anonymized, and then exported them. For certain files, however, the dcm2mnc command is failing and I am receiving the following error when I run it: 'ERROR: Age units (048Y) unknown.' >> >> I am able to convert these dicom files to nifti format with no issue and convert from nifti to dicom fine. I have tried processing the same dicom files in other versions of Horos and have encountered the same error during dcm2mnc. A colleague of mine has been able to preprocess the same dicom files in Horos on his own laptop and was able to subsequently convert them to minc with no problem. I am not sure what is causing the dcm2mnc conversion to fail. >> >> Any help would be much appreciated. >> >> Thanks, >> >> Gavin >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > >------------------------------ > >Message: 3 >Date: Wed, 11 Oct 2017 19:51:21 -0400 >From: "Robert D. Vincent" >To: MINC users mailing list >Subject: Re: [MINC-users] DICOM to MINC conversion error >Message-ID: > >Content-Type: text/plain; charset="UTF-8" > >Hi Gavin, > >That's an old bug in dcm2mnc, it was fixed quite a while back. You can get >the updated version as part of the latest minc toolkit distribution: >https://bic-mni.github.io/ > > -bert > >On Wed, Oct 11, 2017 at 7:29 PM, Gavin Elias >wrote: > >> Hi, >> >> I have been converting dicom files to minc using the dcm2mnc command. I >> preprocessed these dicom files in Horos on my laptop, where I decompressed, >> anonymized, and then exported them. For certain files, however, the >> dcm2mnc command is failing and I am receiving the following error when I >> run it: 'ERROR: Age units (048Y) unknown.' >> >> I am able to convert these dicom files to nifti format with no issue and >> convert from nifti to dicom fine. I have tried processing the same dicom >> files in other versions of Horos and have encountered the same error during >> dcm2mnc. A colleague of mine has been able to preprocess the same dicom >> files in Horos on his own laptop and was able to subsequently convert them >> to minc with no problem. I am not sure what is causing the dcm2mnc >> conversion to fail. >> >> Any help would be much appreciated. >> >> Thanks, >> >> Gavin >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> > > >------------------------------ > >_______________________________________________ >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 145, Issue 1 >****************************************** From zijdenbos at gmail.com Thu Oct 19 22:03:54 2017 From: zijdenbos at gmail.com (Alex Zijdenbos) Date: Thu, 19 Oct 2017 22:03:54 -0400 Subject: [MINC-users] mincstats and ranges that exceed the volume value range Message-ID: Hi all, Thought I'd post this here, in case there is discussion; but I noticed that mincstats' histogram measures can be quite wrong if you happen to specify a range to mincstats that exceeds the range of the volume. An example: $ mincstats -min -max -mean -median mni_icbm152_t1_tal_nlin_sym_09a.mnc *** mincstats - reported min (0.0677952) doesn't equal header (0.0677952) Min: 0.06779524744 Max: 97.32924302 Mean: 28.32028821 Median: *11.22854638* $ mincstats -min -max -mean -median *-ceil 1e6* mni_icbm152_t1_tal_nlin_sym_09a.mnc *** mincstats - reported min (0.0677952) doesn't equal header (0.0677952) Min: 0.06779524744 Max: 97.32924302 Mean: 28.32028821 Median: *500.0677626* The reason for the massive change in the median is that the histogram range/bins are apparently calculated based on the user-supplied range. I would say that this is wrong, and that these should be clamped to the actual range of the volume - especially since mincstats already has -hist_{floor,ceil,range} options with which you could fully control these. -- A From bert at phalarope.com Sat Oct 21 14:03:22 2017 From: bert at phalarope.com (Robert D. Vincent) Date: Sat, 21 Oct 2017 14:03:22 -0400 Subject: [MINC-users] mincstats and ranges that exceed the volume value range In-Reply-To: References: Message-ID: Hi Alex, Thanks for the report - I completely agree that this seems wrong. Looking over the code, I can confirm that the issue arises because we blindly adopt the -floor and -ceil values as defining the histogram range. We can wind up with a histogram with only a single non-empty bin, throwing the calculation off. My first thought would be to ignore a -floor or -ceil value that is outside the reported real range of the volume. I can't think of a situation where this would be incorrect, as long as the header values are close to correct. -bert On Thu, Oct 19, 2017 at 10:03 PM, Alex Zijdenbos wrote: > Hi all, > > Thought I'd post this here, in case there is discussion; but I noticed that > mincstats' histogram measures can be quite wrong if you happen to specify a > range to mincstats that exceeds the range of the volume. > > An example: > > $ mincstats -min -max -mean -median mni_icbm152_t1_tal_nlin_sym_09a.mnc > *** mincstats - reported min (0.0677952) doesn't equal header (0.0677952) > Min: 0.06779524744 > Max: 97.32924302 > Mean: 28.32028821 > Median: *11.22854638* > > $ mincstats -min -max -mean -median *-ceil 1e6* > mni_icbm152_t1_tal_nlin_sym_09a.mnc > *** mincstats - reported min (0.0677952) doesn't equal header (0.0677952) > Min: 0.06779524744 > Max: 97.32924302 > Mean: 28.32028821 > Median: *500.0677626* > > The reason for the massive change in the median is that the histogram > range/bins are apparently calculated based on the user-supplied range. I > would say that this is wrong, and that these should be clamped to the > actual range of the volume - especially since mincstats already has > -hist_{floor,ceil,range} options with which you could fully control these. > > -- A > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >