From waveflux at gmail.com Wed May 3 15:07:45 2017 From: waveflux at gmail.com (waveflux at gmail.com) Date: Wed, 3 May 2017 12:07:45 -0700 Subject: [MINC-users] Tom Beaudry has shared a document on Google Docs with you Message-ID: Tom Beaudry has invited you to view the following document: Open in Docs From jon at pipitone.ca Sat May 6 14:02:30 2017 From: jon at pipitone.ca (Jon Pipitone) Date: Sat, 06 May 2017 14:02:30 -0400 Subject: [MINC-users] Tom Beaudry has shared a document on Google Docs with you In-Reply-To: References: Message-ID: <1494093750.2893256.967971496.53FEDFFA@webmail.messagingengine.com> Hi all, This is a phishing attack. It appears like someone has sent you a google doc, but when you attempt to view it you are in fact giving spammers access to your email. See here: https://motherboard.vice.com/?/massive-gmail-google-doc-phi? https://isc.sans.edu/diary/22372 tldr; If you've been caught by this, you'll need to do the following: 1. Go to https://myaccount.google.com/permissions 2. Find the app called "Google Docs" (it's not actually google docs!) 3. Revoke all permissions to it. Jon. On Wed, May 3, 2017, at 03:07 PM, waveflux at gmail.com wrote: > Tom Beaudry has invited you to view the following document: > > Open in Docs > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users From redoute at cermep.fr Thu May 18 09:30:32 2017 From: redoute at cermep.fr (=?UTF-8?B?SsOpcsO0bWUgUmVkb3V0w6k=?=) Date: Thu, 18 May 2017 15:30:32 +0200 Subject: [MINC-users] information loss after mincreshape In-Reply-To: <57752CE4.8080202@cermep.fr> References: <57615DCA.4030009@cermep.fr> <577117BD.7060200@cermep.fr> <57752CE4.8080202@cermep.fr> Message-ID: Hi all, We are facing a new problem with mincreshape while processing dynamic PET data. here is our process: dcm2mnc ==> dyn.mnc mincreshape +xdirection + ydirection +zdirection dyn.mnc tmp.mnc we want then to reorient the image: param2xfm -rotations 90 0 180 dcmPET2mnc.xfm mincresample -transformation dcmPET2mnc.xfm tmp.mnc final.mnc -like template.mnc this last step fails with the following warnings: "Irregular dimension in file tmp.mnc contains non-monotonic or repeated values" "substituting a step size of 1" and the resulting file contains no data If we don't do the mincreshape step ==> no problem with mincresample Any ideas? (we are using the dev branch of Minc tools) Thanks for your help Jerome Le 30/06/2016 ? 16:29, J?r?me Redout? a ?crit : > Thank you! > > I 'm going to test it right now > > Best > Jerome > > Le 30/06/2016 16:18, Robert D. Vincent a ?crit : >> Hi Jerome, >> >> I believe I have fixed the issue. After thinking about it, I believe >> it is >> safe to preserve the information whenever it happens to be present, >> so that >> is now the behavior of mincreshape. >> >> I pushed the fix to the develop branch. >> >> -bert >> >> On Mon, Jun 27, 2016 at 8:10 AM, J?r?me Redout? >> wrote: >> >>> Hi Robert, >>> did you find how to fix the mincreshape bug? >>> thank you >>> Best regards >>> >>> Jerome >>> >>> Le 15/06/2016 19:19, Robert D. Vincent a ?crit : >>> >>>> One thing I'd like to check: is the file you're using a >>>> regularly-sampled >>>> file, i.e. is there a constant time duration for each image? >>>> >>>> >>>> On Wed, Jun 15, 2016 at 1:09 PM, Robert D. Vincent < >>>> robert.d.vincent at mcgill.ca> wrote: >>>> >>>> Hi J?r?me, >>>>> Thanks for the report, I've reproduced it here. It seems that >>>>> mincreshape >>>>> fails to copy the time dimension properly. I will fix it as soon as >>>>> possible. >>>>> >>>>> -bert >>>>> >>>>> On Wed, Jun 15, 2016 at 9:53 AM, J?r?me Redout? >>>>> wrote: >>>>> >>>>> Dear all, >>>>>> I'm processing dynamic PET data acquired on Siemens Biograph mMR. >>>>>> >>>>>> after conversion from DICOM to MINC using dcm2mnc, I can extract >>>>>> frames >>>>>> timings using: >>>>>> >>>>>> mincinfo -varvalue time xxx.mnc >>>>>> >>>>>> BUT, >>>>>> >>>>>> after mincreshape +xdirection +ydirection +zdirection xxx.mnc >>>>>> xxx_res.mnc >>>>>> >>>>>> mincinfo -varvalue time xxx_res.mnc outputs only "0" >>>>>> >>>>>> any ideas about this bug? >>>>>> >>>>>> Thanks >>>>>> Jerome >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> ================================================================== >>>>>> J?r?me Redout? >>>>>> Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1 >>>>>> CERMEP - Imagerie du vivant >>>>>> 59 Bd Pinel. 69677 Bron - FRANCE >>>>>> tel : 33 (0)4 72 68 86 18 (bureau) >>>>>> tel : 33 (0)4 72 68 86 00 (standard) >>>>>> fax : 33 (0)4 72 68 86 10 >>>>>> ================================================================== >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> MINC-users at bic.mni.mcgill.ca >>>>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >>>>>> >>>>>> >>>>> _______________________________________________ >>>> MINC-users at bic.mni.mcgill.ca >>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >>>> >>>> >>> -- >>> ================================================================== >>> J?r?me Redout? >>> Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1 >>> CERMEP - Imagerie du vivant >>> 59 Bd Pinel. 69677 Bron - FRANCE >>> tel : 33 (0)4 72 68 86 18 (bureau) >>> tel : 33 (0)4 72 68 86 00 (standard) >>> fax : 33 (0)4 72 68 86 10 >>> ================================================================== >>> >>> >>> _______________________________________________ >>> MINC-users at bic.mni.mcgill.ca >>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >>> >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> > > From zijdenbos at gmail.com Thu May 18 09:38:01 2017 From: zijdenbos at gmail.com (Alex Zijdenbos) Date: Thu, 18 May 2017 09:38:01 -0400 Subject: [MINC-users] information loss after mincreshape In-Reply-To: References: <57615DCA.4030009@cermep.fr> <577117BD.7060200@cermep.fr> <57752CE4.8080202@cermep.fr> Message-ID: Hi Jerome, Although I don't think this explains what you are seeing, I suspect that this: mincreshape +xdirection + ydirection +zdirection dyn.mnc tmp.mnc may not do what you think it does, due to this, rather non-intuitive, bit in the man page: +direction Flip images to give positive step value for spatial axes. Note that the flipping of spatial axes only applies to "image dimensions". These are the two fastest varying (non-vector) dimensions in the file. If you want to flip a non-image dimension, you can convert it to an image dimension with -dimsize dimname=-1 (the -1 means don't really change the size). Check out the examples. -- A On Thu, May 18, 2017 at 9:30 AM, J?r?me Redout? wrote: > Hi all, > > We are facing a new problem with mincreshape while processing dynamic PET > data. > > here is our process: > > dcm2mnc ==> dyn.mnc > > mincreshape +xdirection + ydirection +zdirection dyn.mnc tmp.mnc > > we want then to reorient the image: > > param2xfm -rotations 90 0 180 dcmPET2mnc.xfm > > mincresample -transformation dcmPET2mnc.xfm tmp.mnc final.mnc -like > template.mnc > > this last step fails with the following warnings: > > "Irregular dimension in file tmp.mnc contains non-monotonic or > repeated values" > > "substituting a step size of 1" > > and the resulting file contains no data > > If we don't do the mincreshape step ==> no problem with mincresample > > Any ideas? > > (we are using the dev branch of Minc tools) > > Thanks for your help > > Jerome > > > > > > Le 30/06/2016 ? 16:29, J?r?me Redout? a ?crit : > >> Thank you! >> >> I 'm going to test it right now >> >> Best >> Jerome >> >> Le 30/06/2016 16:18, Robert D. Vincent a ?crit : >> >>> Hi Jerome, >>> >>> I believe I have fixed the issue. After thinking about it, I believe it >>> is >>> safe to preserve the information whenever it happens to be present, so >>> that >>> is now the behavior of mincreshape. >>> >>> I pushed the fix to the develop branch. >>> >>> -bert >>> >>> On Mon, Jun 27, 2016 at 8:10 AM, J?r?me Redout? >>> wrote: >>> >>> Hi Robert, >>>> did you find how to fix the mincreshape bug? >>>> thank you >>>> Best regards >>>> >>>> Jerome >>>> >>>> Le 15/06/2016 19:19, Robert D. Vincent a ?crit : >>>> >>>> One thing I'd like to check: is the file you're using a >>>>> regularly-sampled >>>>> file, i.e. is there a constant time duration for each image? >>>>> >>>>> >>>>> On Wed, Jun 15, 2016 at 1:09 PM, Robert D. Vincent < >>>>> robert.d.vincent at mcgill.ca> wrote: >>>>> >>>>> Hi J?r?me, >>>>> >>>>>> Thanks for the report, I've reproduced it here. It seems that >>>>>> mincreshape >>>>>> fails to copy the time dimension properly. I will fix it as soon as >>>>>> possible. >>>>>> >>>>>> -bert >>>>>> >>>>>> On Wed, Jun 15, 2016 at 9:53 AM, J?r?me Redout? >>>>>> wrote: >>>>>> >>>>>> Dear all, >>>>>> >>>>>>> I'm processing dynamic PET data acquired on Siemens Biograph mMR. >>>>>>> >>>>>>> after conversion from DICOM to MINC using dcm2mnc, I can extract >>>>>>> frames >>>>>>> timings using: >>>>>>> >>>>>>> mincinfo -varvalue time xxx.mnc >>>>>>> >>>>>>> BUT, >>>>>>> >>>>>>> after mincreshape +xdirection +ydirection +zdirection xxx.mnc >>>>>>> xxx_res.mnc >>>>>>> >>>>>>> mincinfo -varvalue time xxx_res.mnc outputs only "0" >>>>>>> >>>>>>> any ideas about this bug? >>>>>>> >>>>>>> Thanks >>>>>>> Jerome >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> ================================================================== >>>>>>> J?r?me Redout? >>>>>>> Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1 >>>>>>> CERMEP - Imagerie du vivant >>>>>>> 59 Bd Pinel. 69677 Bron - FRANCE >>>>>>> tel : 33 (0)4 72 68 86 18 (bureau) >>>>>>> tel : 33 (0)4 72 68 86 00 (standard) >>>>>>> fax : 33 (0)4 72 68 86 10 >>>>>>> ================================================================== >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> MINC-users at bic.mni.mcgill.ca >>>>>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>> >>>>> MINC-users at bic.mni.mcgill.ca >>>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >>>>> >>>>> >>>>> -- >>>> ================================================================== >>>> J?r?me Redout? >>>> Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1 >>>> CERMEP - Imagerie du vivant >>>> 59 Bd Pinel. 69677 Bron - FRANCE >>>> tel : 33 (0)4 72 68 86 18 (bureau) >>>> tel : 33 (0)4 72 68 86 00 (standard) >>>> fax : 33 (0)4 72 68 86 10 >>>> ================================================================== >>>> >>>> >>>> _______________________________________________ >>>> MINC-users at bic.mni.mcgill.ca >>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >>>> >>>> _______________________________________________ >>> MINC-users at bic.mni.mcgill.ca >>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >>> >>> >> >> > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From redoute at cermep.fr Thu May 18 10:28:02 2017 From: redoute at cermep.fr (=?UTF-8?B?SsOpcsO0bWUgUmVkb3V0w6k=?=) Date: Thu, 18 May 2017 16:28:02 +0200 Subject: [MINC-users] information loss after mincreshape In-Reply-To: References: <57615DCA.4030009@cermep.fr> <577117BD.7060200@cermep.fr> <57752CE4.8080202@cermep.fr> Message-ID: <6b4df586-9b5b-43b2-7d52-126ade2a5c81@cermep.fr> Thank you Alex, Ok, it's still a bit obscure for me: If I understand, one of the 3 dimensions is a non-image dimension? Does it mean that it can only have 2 "image dimensions"? I don't really understand what you mean by "the 2 fastest varying". How can I identify the "non image dimension" thank you Jerome Le 18/05/2017 ? 15:38, Alex Zijdenbos a ?crit : > Hi Jerome, > > Although I don't think this explains what you are seeing, I suspect that > this: > > mincreshape +xdirection + ydirection +zdirection dyn.mnc tmp.mnc > > may not do what you think it does, due to this, rather non-intuitive, bit > in the man page: > > +direction > Flip images to give positive step value for spatial axes. > Note that the flipping of spatial axes only applies to "image dimensions". > These are the two fastest > varying (non-vector) dimensions in the file. If you want to > flip a non-image dimension, you can convert it to an image dimension with > -dimsize dimname=-1 (the -1 > means don't really change the size). Check out the examples. > > -- A > > > On Thu, May 18, 2017 at 9:30 AM, J?r?me Redout? wrote: > >> Hi all, >> >> We are facing a new problem with mincreshape while processing dynamic PET >> data. >> >> here is our process: >> >> dcm2mnc ==> dyn.mnc >> >> mincreshape +xdirection + ydirection +zdirection dyn.mnc tmp.mnc >> >> we want then to reorient the image: >> >> param2xfm -rotations 90 0 180 dcmPET2mnc.xfm >> >> mincresample -transformation dcmPET2mnc.xfm tmp.mnc final.mnc -like >> template.mnc >> >> this last step fails with the following warnings: >> >> "Irregular dimension in file tmp.mnc contains non-monotonic or >> repeated values" >> >> "substituting a step size of 1" >> >> and the resulting file contains no data >> >> If we don't do the mincreshape step ==> no problem with mincresample >> >> Any ideas? >> >> (we are using the dev branch of Minc tools) >> >> Thanks for your help >> >> Jerome >> >> >> >> >> >> Le 30/06/2016 ? 16:29, J?r?me Redout? a ?crit : >> >>> Thank you! >>> >>> I 'm going to test it right now >>> >>> Best >>> Jerome >>> >>> Le 30/06/2016 16:18, Robert D. Vincent a ?crit : >>> >>>> Hi Jerome, >>>> >>>> I believe I have fixed the issue. After thinking about it, I believe it >>>> is >>>> safe to preserve the information whenever it happens to be present, so >>>> that >>>> is now the behavior of mincreshape. >>>> >>>> I pushed the fix to the develop branch. >>>> >>>> -bert >>>> >>>> On Mon, Jun 27, 2016 at 8:10 AM, J?r?me Redout? >>>> wrote: >>>> >>>> Hi Robert, >>>>> did you find how to fix the mincreshape bug? >>>>> thank you >>>>> Best regards >>>>> >>>>> Jerome >>>>> >>>>> Le 15/06/2016 19:19, Robert D. Vincent a ?crit : >>>>> >>>>> One thing I'd like to check: is the file you're using a >>>>>> regularly-sampled >>>>>> file, i.e. is there a constant time duration for each image? >>>>>> >>>>>> >>>>>> On Wed, Jun 15, 2016 at 1:09 PM, Robert D. Vincent < >>>>>> robert.d.vincent at mcgill.ca> wrote: >>>>>> >>>>>> Hi J?r?me, >>>>>> >>>>>>> Thanks for the report, I've reproduced it here. It seems that >>>>>>> mincreshape >>>>>>> fails to copy the time dimension properly. I will fix it as soon as >>>>>>> possible. >>>>>>> >>>>>>> -bert >>>>>>> >>>>>>> On Wed, Jun 15, 2016 at 9:53 AM, J?r?me Redout? >>>>>>> wrote: >>>>>>> >>>>>>> Dear all, >>>>>>> >>>>>>>> I'm processing dynamic PET data acquired on Siemens Biograph mMR. >>>>>>>> >>>>>>>> after conversion from DICOM to MINC using dcm2mnc, I can extract >>>>>>>> frames >>>>>>>> timings using: >>>>>>>> >>>>>>>> mincinfo -varvalue time xxx.mnc >>>>>>>> >>>>>>>> BUT, >>>>>>>> >>>>>>>> after mincreshape +xdirection +ydirection +zdirection xxx.mnc >>>>>>>> xxx_res.mnc >>>>>>>> >>>>>>>> mincinfo -varvalue time xxx_res.mnc outputs only "0" >>>>>>>> >>>>>>>> any ideas about this bug? >>>>>>>> >>>>>>>> Thanks >>>>>>>> Jerome >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> ================================================================== >>>>>>>> J?r?me Redout? >>>>>>>> Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1 >>>>>>>> CERMEP - Imagerie du vivant >>>>>>>> 59 Bd Pinel. 69677 Bron - FRANCE >>>>>>>> tel : 33 (0)4 72 68 86 18 (bureau) >>>>>>>> tel : 33 (0)4 72 68 86 00 (standard) >>>>>>>> fax : 33 (0)4 72 68 86 10 >>>>>>>> ================================================================== >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> MINC-users at bic.mni.mcgill.ca >>>>>>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>> MINC-users at bic.mni.mcgill.ca >>>>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >>>>>> >>>>>> >>>>>> -- >>>>> ================================================================== >>>>> J?r?me Redout? >>>>> Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1 >>>>> CERMEP - Imagerie du vivant >>>>> 59 Bd Pinel. 69677 Bron - FRANCE >>>>> tel : 33 (0)4 72 68 86 18 (bureau) >>>>> tel : 33 (0)4 72 68 86 00 (standard) >>>>> fax : 33 (0)4 72 68 86 10 >>>>> ================================================================== >>>>> >>>>> >>>>> _______________________________________________ >>>>> MINC-users at bic.mni.mcgill.ca >>>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >>>>> >>>>> _______________________________________________ >>>> MINC-users at bic.mni.mcgill.ca >>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >>>> >>>> >>> >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From vladimir.fonov at gmail.com Thu May 18 10:49:34 2017 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Thu, 18 May 2017 10:49:34 -0400 Subject: [MINC-users] information loss after mincreshape In-Reply-To: <6b4df586-9b5b-43b2-7d52-126ade2a5c81@cermep.fr> References: <57615DCA.4030009@cermep.fr> <577117BD.7060200@cermep.fr> <57752CE4.8080202@cermep.fr> <6b4df586-9b5b-43b2-7d52-126ade2a5c81@cermep.fr> Message-ID: <5f9969bb-c045-b558-398b-be7a682b0b59@gmail.com> It's a "feature" of mincreshape: http://www.bic.mni.mcgill.ca/pipermail/minc-users/2015-March/004020.html It bites people at the rate of approximately once per year. Your resampling problem might be something completely different. Like a bug in mincresample when treating 4D volumes. On 2017-05-18 10:28 AM, J?r?me Redout? wrote: > Thank you Alex, > > Ok, it's still a bit obscure for me: > > If I understand, one of the 3 dimensions is a non-image dimension? > > Does it mean that it can only have 2 "image dimensions"? > > I don't really understand what you mean by "the 2 fastest varying". How > can I identify the "non image dimension" > > thank you > > Jerome > > > > > Le 18/05/2017 ? 15:38, Alex Zijdenbos a ?crit : >> Hi Jerome, >> >> Although I don't think this explains what you are seeing, I suspect that >> this: >> >> mincreshape +xdirection + ydirection +zdirection dyn.mnc tmp.mnc >> >> may not do what you think it does, due to this, rather non-intuitive, bit >> in the man page: >> >> +direction >> Flip images to give positive step value for spatial axes. >> Note that the flipping of spatial axes only applies to "image >> dimensions". >> These are the two fastest >> varying (non-vector) dimensions in the file. If you >> want to >> flip a non-image dimension, you can convert it to an image dimension with >> -dimsize dimname=-1 (the -1 >> means don't really change the size). Check out the >> examples. >> >> -- A >> >> >> On Thu, May 18, 2017 at 9:30 AM, J?r?me Redout? >> wrote: >> >>> Hi all, >>> >>> We are facing a new problem with mincreshape while processing dynamic >>> PET >>> data. >>> >>> here is our process: >>> >>> dcm2mnc ==> dyn.mnc >>> >>> mincreshape +xdirection + ydirection +zdirection dyn.mnc tmp.mnc >>> >>> we want then to reorient the image: >>> >>> param2xfm -rotations 90 0 180 dcmPET2mnc.xfm >>> >>> mincresample -transformation dcmPET2mnc.xfm tmp.mnc final.mnc -like >>> template.mnc >>> >>> this last step fails with the following warnings: >>> >>> "Irregular dimension in file tmp.mnc contains non-monotonic or >>> repeated values" >>> >>> "substituting a step size of 1" >>> >>> and the resulting file contains no data >>> >>> If we don't do the mincreshape step ==> no problem with mincresample >>> >>> Any ideas? >>> >>> (we are using the dev branch of Minc tools) >>> >>> Thanks for your help >>> >>> Jerome >>> >>> >>> >>> >>> >>> Le 30/06/2016 ? 16:29, J?r?me Redout? a ?crit : >>> >>>> Thank you! >>>> >>>> I 'm going to test it right now >>>> >>>> Best >>>> Jerome >>>> >>>> Le 30/06/2016 16:18, Robert D. Vincent a ?crit : >>>> >>>>> Hi Jerome, >>>>> >>>>> I believe I have fixed the issue. After thinking about it, I >>>>> believe it >>>>> is >>>>> safe to preserve the information whenever it happens to be present, so >>>>> that >>>>> is now the behavior of mincreshape. >>>>> >>>>> I pushed the fix to the develop branch. >>>>> >>>>> -bert >>>>> >>>>> On Mon, Jun 27, 2016 at 8:10 AM, J?r?me Redout? >>>>> wrote: >>>>> >>>>> Hi Robert, >>>>>> did you find how to fix the mincreshape bug? >>>>>> thank you >>>>>> Best regards >>>>>> >>>>>> Jerome >>>>>> >>>>>> Le 15/06/2016 19:19, Robert D. Vincent a ?crit : >>>>>> >>>>>> One thing I'd like to check: is the file you're using a >>>>>>> regularly-sampled >>>>>>> file, i.e. is there a constant time duration for each image? >>>>>>> >>>>>>> >>>>>>> On Wed, Jun 15, 2016 at 1:09 PM, Robert D. Vincent < >>>>>>> robert.d.vincent at mcgill.ca> wrote: >>>>>>> >>>>>>> Hi J?r?me, >>>>>>> >>>>>>>> Thanks for the report, I've reproduced it here. It seems that >>>>>>>> mincreshape >>>>>>>> fails to copy the time dimension properly. I will fix it as soon as >>>>>>>> possible. >>>>>>>> >>>>>>>> -bert >>>>>>>> >>>>>>>> On Wed, Jun 15, 2016 at 9:53 AM, J?r?me Redout? >>>>>>>> wrote: >>>>>>>> >>>>>>>> Dear all, >>>>>>>> >>>>>>>>> I'm processing dynamic PET data acquired on Siemens Biograph mMR. >>>>>>>>> >>>>>>>>> after conversion from DICOM to MINC using dcm2mnc, I can extract >>>>>>>>> frames >>>>>>>>> timings using: >>>>>>>>> >>>>>>>>> mincinfo -varvalue time xxx.mnc >>>>>>>>> >>>>>>>>> BUT, >>>>>>>>> >>>>>>>>> after mincreshape +xdirection +ydirection +zdirection xxx.mnc >>>>>>>>> xxx_res.mnc >>>>>>>>> >>>>>>>>> mincinfo -varvalue time xxx_res.mnc outputs only "0" >>>>>>>>> >>>>>>>>> any ideas about this bug? >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> Jerome >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> ================================================================== >>>>>>>>> J?r?me Redout? >>>>>>>>> Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1 >>>>>>>>> CERMEP - Imagerie du vivant >>>>>>>>> 59 Bd Pinel. 69677 Bron - FRANCE >>>>>>>>> tel : 33 (0)4 72 68 86 18 (bureau) >>>>>>>>> tel : 33 (0)4 72 68 86 00 (standard) >>>>>>>>> fax : 33 (0)4 72 68 86 10 >>>>>>>>> ================================================================== >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> MINC-users at bic.mni.mcgill.ca >>>>>>>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>> MINC-users at bic.mni.mcgill.ca >>>>>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >>>>>>> >>>>>>> >>>>>>> -- >>>>>> ================================================================== >>>>>> J?r?me Redout? >>>>>> Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1 >>>>>> CERMEP - Imagerie du vivant >>>>>> 59 Bd Pinel. 69677 Bron - FRANCE >>>>>> tel : 33 (0)4 72 68 86 18 (bureau) >>>>>> tel : 33 (0)4 72 68 86 00 (standard) >>>>>> fax : 33 (0)4 72 68 86 10 >>>>>> ================================================================== >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> MINC-users at bic.mni.mcgill.ca >>>>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >>>>>> >>>>>> _______________________________________________ >>>>> MINC-users at bic.mni.mcgill.ca >>>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >>>>> >>>>> >>>> >>> _______________________________________________ >>> MINC-users at bic.mni.mcgill.ca >>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >>> >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> > > _______________________________________________ > 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 mishkind at gmail.com Thu May 18 15:47:29 2017 From: mishkind at gmail.com (Mishkin Derakhshan) Date: Thu, 18 May 2017 09:47:29 -1000 Subject: [MINC-users] minc file is not visible in register but is visible in Display Message-ID: Hi, I have a file that when viewed in register is not viewable at all. It is just blank (black) everywhere no matter what I do with the windowing. When I load it in Display it is just fine, so I know the data is there. It is a systemic problem, i.e., all files that are created with my script have this problem of not being visible in register. I'm wondering if it has something to do with the range of my data because if I do further operations on it, then the downstream files load okay. For example, the file that currently does not load is subject_t2map.mnc.gz which contains float values from 0 to 1. If I do something like this, then the resulting 100.mnc loads just fine in register: minccalc -expr 'A[0]*100' subject_t2map.mnc.gz 100.mnc Here are the mincstats of my file with/without a mask: localhost[~/nrx/t2map]$ mincstats subject_t2map.mnc.gz File: subject_t2map.mnc.gz Mask file: (null) Total voxels: 3932160 # voxels: 2178980 % of total: 55.41432699 Volume (mm3): 6536940 Min: 0 Max: 0.9998887777 Sum: 415156.0653 Sum^2: 161711.3365 Mean: 0.1905277081 Variance: 0.03791344611 Stddev: 0.1947137543 CoM_voxel(z,y,x): 30.68098471 128.9858818 128.9017075 CoM_real(x,y,z): 2.09258826 70.06459185 43.54402081 Histogram: (null) Total voxels: 3932160 # voxels: 2178980 % of total: 55.41432699 Median: 0.1142372932 Majority: 0.0002499721886 BiModalT: 0.3392122686 PctT [ 0%]: 0.0002499721886 Entropy : 9.187178001 localhost[~/nrx/t2map]$ mincstats subject_t2map.mnc.gz -mask subject_t2map_mask.mnc.gz -mask_binvalue 1.0 File: subject_t2map.mnc.gz Mask file: subject_t2map_mask.mnc.gz Total voxels: 3932160 # voxels: 1962553 % of total: 49.91030375 Volume (mm3): 5887659 Min: 0.01020694431 Max: 0.9998887777 Sum: 415156.0653 Sum^2: 161711.3365 Mean: 0.211538779 Variance: 0.0376498199 Stddev: 0.194035615 CoM_voxel(z,y,x): 30.68098471 128.9858818 128.9017075 CoM_real(x,y,z): 2.09258826 70.06459185 43.54402081 Histogram: (null) Total voxels: 3932160 # voxels: 1962553 % of total: 49.91030375 Median: 0.1242361822 Majority: 0.09273968637 BiModalT: 0.3552104831 PctT [ 0%]: 0.0002499721886 Entropy : 9.681988728 And here is the full mincheader: localhost[~/nrx/t2map]$ mincheader subject_t2map.mnc.gz netcdf mincheader-18621-tmp { dimensions: zspace = 60 ; yspace = 256 ; xspace = 256 ; variables: double zspace(zspace) ; zspace:varid = "MINC standard variable" ; zspace:vartype = "dimension____" ; zspace:version = "MINC Version 1.0" ; zspace:comments = "Z increases from patient inferior to superior" ; zspace:spacing = "regular__" ; zspace:alignment = "centre" ; zspace:step = 3. ; zspace:start = -53.5106888535874 ; zspace:spacetype = "native____" ; zspace:direction_cosines = 0.00888470442653803, -0.0702364344961855, 0.997490804617524 ; int yspace ; yspace:varid = "MINC standard variable" ; yspace:vartype = "dimension____" ; yspace:version = "MINC Version 1.0" ; yspace:comments = "Y increases from patient posterior to anterior" ; yspace:spacing = "regular__" ; yspace:alignment = "centre" ; yspace:step = -1. ; yspace:start = 201.955416409066 ; yspace:spacetype = "native____" ; yspace:direction_cosines = 0.0303997023189596, 0.997088076060185, 0.0699373053349794 ; int xspace ; xspace:varid = "MINC standard variable" ; xspace:vartype = "dimension____" ; xspace:version = "MINC Version 1.0" ; xspace:comments = "X increases from patient left to right" ; xspace:spacing = "regular__" ; xspace:alignment = "centre" ; xspace:step = -1. ; xspace:start = 128.433460913677 ; xspace:spacetype = "native____" ; xspace:direction_cosines = 0.999498332440992, -0.0297021098791549, -0.0109940036566919 ; double image-max(zspace) ; image-max:varid = "MINC standard variable" ; image-max:vartype = "var_attribute" ; image-max:version = "MINC Version 1.0" ; image-max:_FillValue = 1. ; image-max:parent = "image" ; double image-min(zspace) ; image-min:varid = "MINC standard variable" ; image-min:vartype = "var_attribute" ; image-min:version = "MINC Version 1.0" ; image-min:_FillValue = 0. ; image-min:parent = "image" ; float image(zspace, yspace, xspace) ; image:parent = "rootvariable" ; image:varid = "MINC standard variable" ; image:vartype = "group________" ; image:version = "MINC Version 1.0" ; image:image-max = "--->image-max" ; image:image-min = "--->image-min" ; image:valid_range = 0.f, 0.9998888f ; image:complete = "true_" ; int rootvariable ; rootvariable:varid = "MINC standard variable" ; rootvariable:vartype = "group________" ; rootvariable:version = "MINC Version 1.0" ; rootvariable:parent = "" ; rootvariable:children = "image" ; // global attributes: :ident = "redacted" ; :minc_version = "2.2.00" ; :history = "Thu Jan 19 10:55:35 2017>>> mincmath -clobber -mult subject_t2map_mask.mnc TMP6_t2map_unclamped.mnc subject_t2map.mnc\n", "" ; } And here is my minc package info stuff: localhost[~/nrx/t2map]$ which register /opt/minc-toolkit/0.3.16/bin/register localhost[~/nrx/t2map]$ register -version register: Version: 1.4.00 localhost[~/nrx/t2map]$ mincstats -version program: 2.2.00 libminc: 2.2.00 netcdf : 4.2.1 of Feb 19 2015 15:50:30 $ HDF5 : 1.8.8 localhost[~/nrx/t2map]$ cat /etc/system-release CentOS release 6.5 (Final) localhost[~/nrx/t2map]$ uname -a Linux localhost.localdomain 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux Any come across this bug before? Any ideas on how to fix it so it is viewable in register? From vladimir.fonov at gmail.com Thu May 18 16:02:39 2017 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Thu, 18 May 2017 16:02:39 -0400 Subject: [MINC-users] minc file is not visible in register but is visible in Display In-Reply-To: References: Message-ID: <01b1f15a-f71c-e209-7a68-1ff89350e0c9@gmail.com> It's a bug in certain versions of register, affecting it's ability to show files stored in float, with low values. Can be fixed by mincreshape -short On 2017-05-18 03:47 PM, Mishkin Derakhshan wrote: > Hi, > I have a file that when viewed in register is not viewable at all. It is > just blank (black) everywhere no matter what I do with the windowing. > When I load it in Display it is just fine, so I know the data is there. > > It is a systemic problem, i.e., all files that are created with my script > have this problem of not being visible in register. > > I'm wondering if it has something to do with the range of my data because > if I do further operations on it, then the downstream files load okay. > > For example, the file that currently does not load is subject_t2map.mnc.gz > which contains float values from 0 to 1. > > If I do something like this, then the resulting 100.mnc loads just fine in > register: > minccalc -expr 'A[0]*100' subject_t2map.mnc.gz 100.mnc > > Here are the mincstats of my file with/without a mask: > > localhost[~/nrx/t2map]$ mincstats subject_t2map.mnc.gz > File: subject_t2map.mnc.gz > Mask file: (null) > Total voxels: 3932160 > # voxels: 2178980 > % of total: 55.41432699 > Volume (mm3): 6536940 > Min: 0 > Max: 0.9998887777 > Sum: 415156.0653 > Sum^2: 161711.3365 > Mean: 0.1905277081 > Variance: 0.03791344611 > Stddev: 0.1947137543 > CoM_voxel(z,y,x): 30.68098471 128.9858818 128.9017075 > CoM_real(x,y,z): 2.09258826 70.06459185 43.54402081 > > Histogram: (null) > Total voxels: 3932160 > # voxels: 2178980 > % of total: 55.41432699 > Median: 0.1142372932 > Majority: 0.0002499721886 > BiModalT: 0.3392122686 > PctT [ 0%]: 0.0002499721886 > Entropy : 9.187178001 > > localhost[~/nrx/t2map]$ mincstats subject_t2map.mnc.gz -mask > subject_t2map_mask.mnc.gz -mask_binvalue 1.0 > File: subject_t2map.mnc.gz > Mask file: subject_t2map_mask.mnc.gz > Total voxels: 3932160 > # voxels: 1962553 > % of total: 49.91030375 > Volume (mm3): 5887659 > Min: 0.01020694431 > Max: 0.9998887777 > Sum: 415156.0653 > Sum^2: 161711.3365 > Mean: 0.211538779 > Variance: 0.0376498199 > Stddev: 0.194035615 > CoM_voxel(z,y,x): 30.68098471 128.9858818 128.9017075 > CoM_real(x,y,z): 2.09258826 70.06459185 43.54402081 > > Histogram: (null) > Total voxels: 3932160 > # voxels: 1962553 > % of total: 49.91030375 > Median: 0.1242361822 > Majority: 0.09273968637 > BiModalT: 0.3552104831 > PctT [ 0%]: 0.0002499721886 > Entropy : 9.681988728 > > > And here is the full mincheader: > localhost[~/nrx/t2map]$ mincheader subject_t2map.mnc.gz > netcdf mincheader-18621-tmp { > dimensions: > zspace = 60 ; > yspace = 256 ; > xspace = 256 ; > variables: > double zspace(zspace) ; > zspace:varid = "MINC standard variable" ; > zspace:vartype = "dimension____" ; > zspace:version = "MINC Version 1.0" ; > zspace:comments = "Z increases from patient inferior to superior" ; > zspace:spacing = "regular__" ; > zspace:alignment = "centre" ; > zspace:step = 3. ; > zspace:start = -53.5106888535874 ; > zspace:spacetype = "native____" ; > zspace:direction_cosines = 0.00888470442653803, -0.0702364344961855, > 0.997490804617524 ; > int yspace ; > yspace:varid = "MINC standard variable" ; > yspace:vartype = "dimension____" ; > yspace:version = "MINC Version 1.0" ; > yspace:comments = "Y increases from patient posterior to anterior" ; > yspace:spacing = "regular__" ; > yspace:alignment = "centre" ; > yspace:step = -1. ; > yspace:start = 201.955416409066 ; > yspace:spacetype = "native____" ; > yspace:direction_cosines = 0.0303997023189596, 0.997088076060185, > 0.0699373053349794 ; > int xspace ; > xspace:varid = "MINC standard variable" ; > xspace:vartype = "dimension____" ; > xspace:version = "MINC Version 1.0" ; > xspace:comments = "X increases from patient left to right" ; > xspace:spacing = "regular__" ; > xspace:alignment = "centre" ; > xspace:step = -1. ; > xspace:start = 128.433460913677 ; > xspace:spacetype = "native____" ; > xspace:direction_cosines = 0.999498332440992, -0.0297021098791549, > -0.0109940036566919 ; > double image-max(zspace) ; > image-max:varid = "MINC standard variable" ; > image-max:vartype = "var_attribute" ; > image-max:version = "MINC Version 1.0" ; > image-max:_FillValue = 1. ; > image-max:parent = "image" ; > double image-min(zspace) ; > image-min:varid = "MINC standard variable" ; > image-min:vartype = "var_attribute" ; > image-min:version = "MINC Version 1.0" ; > image-min:_FillValue = 0. ; > image-min:parent = "image" ; > float image(zspace, yspace, xspace) ; > image:parent = "rootvariable" ; > image:varid = "MINC standard variable" ; > image:vartype = "group________" ; > image:version = "MINC Version 1.0" ; > image:image-max = "--->image-max" ; > image:image-min = "--->image-min" ; > image:valid_range = 0.f, 0.9998888f ; > image:complete = "true_" ; > int rootvariable ; > rootvariable:varid = "MINC standard variable" ; > rootvariable:vartype = "group________" ; > rootvariable:version = "MINC Version 1.0" ; > rootvariable:parent = "" ; > rootvariable:children = "image" ; > > // global attributes: > :ident = "redacted" ; > :minc_version = "2.2.00" ; > :history = "Thu Jan 19 10:55:35 2017>>> mincmath -clobber -mult > subject_t2map_mask.mnc TMP6_t2map_unclamped.mnc subject_t2map.mnc\n", > "" ; > } > > > And here is my minc package info stuff: > localhost[~/nrx/t2map]$ which register > /opt/minc-toolkit/0.3.16/bin/register > > localhost[~/nrx/t2map]$ register -version > register: Version: 1.4.00 > > localhost[~/nrx/t2map]$ mincstats -version > program: 2.2.00 > libminc: 2.2.00 > netcdf : 4.2.1 of Feb 19 2015 15:50:30 $ > HDF5 : 1.8.8 > > localhost[~/nrx/t2map]$ cat /etc/system-release > CentOS release 6.5 (Final) > > localhost[~/nrx/t2map]$ uname -a > Linux localhost.localdomain 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 > 21:14:45 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > > Any come across this bug before? Any ideas on how to fix it so it is > viewable in register? > _______________________________________________ > 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 zijdenbos at gmail.com Thu May 18 18:37:48 2017 From: zijdenbos at gmail.com (Alex Zijdenbos) Date: Thu, 18 May 2017 18:37:48 -0400 Subject: [MINC-users] minc file is not visible in register but is visible in Display In-Reply-To: <01b1f15a-f71c-e209-7a68-1ff89350e0c9@gmail.com> References: <01b1f15a-f71c-e209-7a68-1ff89350e0c9@gmail.com> Message-ID: Bert can probably be more specific, but there is a (more recent?) version of register that does the right thing on volumes like this. On Thu, May 18, 2017 at 4:02 PM, Vladimir S. FONOV wrote: > It's a bug in certain versions of register, affecting it's ability to show > files stored in float, with low values. > Can be fixed by mincreshape -short > > > > On 2017-05-18 03:47 PM, Mishkin Derakhshan wrote: > >> Hi, >> I have a file that when viewed in register is not viewable at all. It is >> just blank (black) everywhere no matter what I do with the windowing. >> When I load it in Display it is just fine, so I know the data is there. >> >> It is a systemic problem, i.e., all files that are created with my script >> have this problem of not being visible in register. >> >> I'm wondering if it has something to do with the range of my data because >> if I do further operations on it, then the downstream files load okay. >> >> For example, the file that currently does not load is subject_t2map.mnc.gz >> which contains float values from 0 to 1. >> >> If I do something like this, then the resulting 100.mnc loads just fine in >> register: >> minccalc -expr 'A[0]*100' subject_t2map.mnc.gz 100.mnc >> >> Here are the mincstats of my file with/without a mask: >> >> localhost[~/nrx/t2map]$ mincstats subject_t2map.mnc.gz >> File: subject_t2map.mnc.gz >> Mask file: (null) >> Total voxels: 3932160 >> # voxels: 2178980 >> % of total: 55.41432699 >> Volume (mm3): 6536940 >> Min: 0 >> Max: 0.9998887777 >> Sum: 415156.0653 >> Sum^2: 161711.3365 >> Mean: 0.1905277081 >> Variance: 0.03791344611 >> Stddev: 0.1947137543 >> CoM_voxel(z,y,x): 30.68098471 128.9858818 128.9017075 >> CoM_real(x,y,z): 2.09258826 70.06459185 43.54402081 >> >> Histogram: (null) >> Total voxels: 3932160 >> # voxels: 2178980 >> % of total: 55.41432699 >> Median: 0.1142372932 >> Majority: 0.0002499721886 >> BiModalT: 0.3392122686 >> PctT [ 0%]: 0.0002499721886 >> Entropy : 9.187178001 >> >> localhost[~/nrx/t2map]$ mincstats subject_t2map.mnc.gz -mask >> subject_t2map_mask.mnc.gz -mask_binvalue 1.0 >> File: subject_t2map.mnc.gz >> Mask file: subject_t2map_mask.mnc.gz >> Total voxels: 3932160 >> # voxels: 1962553 >> % of total: 49.91030375 >> Volume (mm3): 5887659 >> Min: 0.01020694431 >> Max: 0.9998887777 >> Sum: 415156.0653 >> Sum^2: 161711.3365 >> Mean: 0.211538779 >> Variance: 0.0376498199 >> Stddev: 0.194035615 >> CoM_voxel(z,y,x): 30.68098471 128.9858818 128.9017075 >> CoM_real(x,y,z): 2.09258826 70.06459185 43.54402081 >> >> Histogram: (null) >> Total voxels: 3932160 >> # voxels: 1962553 >> % of total: 49.91030375 >> Median: 0.1242361822 >> Majority: 0.09273968637 >> BiModalT: 0.3552104831 >> PctT [ 0%]: 0.0002499721886 >> Entropy : 9.681988728 >> >> >> And here is the full mincheader: >> localhost[~/nrx/t2map]$ mincheader subject_t2map.mnc.gz >> netcdf mincheader-18621-tmp { >> dimensions: >> zspace = 60 ; >> yspace = 256 ; >> xspace = 256 ; >> variables: >> double zspace(zspace) ; >> zspace:varid = "MINC standard variable" ; >> zspace:vartype = "dimension____" ; >> zspace:version = "MINC Version 1.0" ; >> zspace:comments = "Z increases from patient inferior to superior" ; >> zspace:spacing = "regular__" ; >> zspace:alignment = "centre" ; >> zspace:step = 3. ; >> zspace:start = -53.5106888535874 ; >> zspace:spacetype = "native____" ; >> zspace:direction_cosines = 0.00888470442653803, -0.0702364344961855, >> 0.997490804617524 ; >> int yspace ; >> yspace:varid = "MINC standard variable" ; >> yspace:vartype = "dimension____" ; >> yspace:version = "MINC Version 1.0" ; >> yspace:comments = "Y increases from patient posterior to anterior" ; >> yspace:spacing = "regular__" ; >> yspace:alignment = "centre" ; >> yspace:step = -1. ; >> yspace:start = 201.955416409066 ; >> yspace:spacetype = "native____" ; >> yspace:direction_cosines = 0.0303997023189596, 0.997088076060185, >> 0.0699373053349794 ; >> int xspace ; >> xspace:varid = "MINC standard variable" ; >> xspace:vartype = "dimension____" ; >> xspace:version = "MINC Version 1.0" ; >> xspace:comments = "X increases from patient left to right" ; >> xspace:spacing = "regular__" ; >> xspace:alignment = "centre" ; >> xspace:step = -1. ; >> xspace:start = 128.433460913677 ; >> xspace:spacetype = "native____" ; >> xspace:direction_cosines = 0.999498332440992, -0.0297021098791549, >> -0.0109940036566919 ; >> double image-max(zspace) ; >> image-max:varid = "MINC standard variable" ; >> image-max:vartype = "var_attribute" ; >> image-max:version = "MINC Version 1.0" ; >> image-max:_FillValue = 1. ; >> image-max:parent = "image" ; >> double image-min(zspace) ; >> image-min:varid = "MINC standard variable" ; >> image-min:vartype = "var_attribute" ; >> image-min:version = "MINC Version 1.0" ; >> image-min:_FillValue = 0. ; >> image-min:parent = "image" ; >> float image(zspace, yspace, xspace) ; >> image:parent = "rootvariable" ; >> image:varid = "MINC standard variable" ; >> image:vartype = "group________" ; >> image:version = "MINC Version 1.0" ; >> image:image-max = "--->image-max" ; >> image:image-min = "--->image-min" ; >> image:valid_range = 0.f, 0.9998888f ; >> image:complete = "true_" ; >> int rootvariable ; >> rootvariable:varid = "MINC standard variable" ; >> rootvariable:vartype = "group________" ; >> rootvariable:version = "MINC Version 1.0" ; >> rootvariable:parent = "" ; >> rootvariable:children = "image" ; >> >> // global attributes: >> :ident = "redacted" ; >> :minc_version = "2.2.00" ; >> :history = "Thu Jan 19 10:55:35 2017>>> mincmath -clobber -mult >> subject_t2map_mask.mnc TMP6_t2map_unclamped.mnc subject_t2map.mnc\n", >> "" ; >> } >> >> >> And here is my minc package info stuff: >> localhost[~/nrx/t2map]$ which register >> /opt/minc-toolkit/0.3.16/bin/register >> >> localhost[~/nrx/t2map]$ register -version >> register: Version: 1.4.00 >> >> localhost[~/nrx/t2map]$ mincstats -version >> program: 2.2.00 >> libminc: 2.2.00 >> netcdf : 4.2.1 of Feb 19 2015 15:50:30 $ >> HDF5 : 1.8.8 >> >> localhost[~/nrx/t2map]$ cat /etc/system-release >> CentOS release 6.5 (Final) >> >> localhost[~/nrx/t2map]$ uname -a >> Linux localhost.localdomain 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 >> 21:14:45 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux >> >> Any come across this bug before? Any ideas on how to fix it so it is >> viewable in register? >> _______________________________________________ >> 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 at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > From bert at phalarope.com Thu May 18 18:47:25 2017 From: bert at phalarope.com (Robert D. Vincent) Date: Thu, 18 May 2017 18:47:25 -0400 Subject: [MINC-users] minc file is not visible in register but is visible in Display In-Reply-To: References: <01b1f15a-f71c-e209-7a68-1ff89350e0c9@gmail.com> Message-ID: Hi, Sorry, I replied to this earlier but used the wrong email address, so that message is probably awaiting moderation. A more recent version of Register might help. Some versions can't deal with float volumes in the range 0-1. Anything built off the current develop branch should be fine. I'm not certain it will help with your version, but it might be useful to try this: register -global Volume_voxel_type 0 subject_t2map.mnc.gz -bert On Thu, May 18, 2017 at 6:37 PM, Alex Zijdenbos wrote: > Bert can probably be more specific, but there is a (more recent?) version > of register that does the right thing on volumes like this. > > On Thu, May 18, 2017 at 4:02 PM, Vladimir S. FONOV < > vladimir.fonov at gmail.com > > wrote: > > > It's a bug in certain versions of register, affecting it's ability to > show > > files stored in float, with low values. > > Can be fixed by mincreshape -short > > > > > > > > On 2017-05-18 03:47 PM, Mishkin Derakhshan wrote: > > > >> Hi, > >> I have a file that when viewed in register is not viewable at all. It is > >> just blank (black) everywhere no matter what I do with the windowing. > >> When I load it in Display it is just fine, so I know the data is there. > >> > >> It is a systemic problem, i.e., all files that are created with my > script > >> have this problem of not being visible in register. > >> > >> I'm wondering if it has something to do with the range of my data > because > >> if I do further operations on it, then the downstream files load okay. > >> > >> For example, the file that currently does not load is > subject_t2map.mnc.gz > >> which contains float values from 0 to 1. > >> > >> If I do something like this, then the resulting 100.mnc loads just fine > in > >> register: > >> minccalc -expr 'A[0]*100' subject_t2map.mnc.gz 100.mnc > >> > >> Here are the mincstats of my file with/without a mask: > >> > >> localhost[~/nrx/t2map]$ mincstats subject_t2map.mnc.gz > >> File: subject_t2map.mnc.gz > >> Mask file: (null) > >> Total voxels: 3932160 > >> # voxels: 2178980 > >> % of total: 55.41432699 > >> Volume (mm3): 6536940 > >> Min: 0 > >> Max: 0.9998887777 > >> Sum: 415156.0653 > >> Sum^2: 161711.3365 > >> Mean: 0.1905277081 > >> Variance: 0.03791344611 > >> Stddev: 0.1947137543 > >> CoM_voxel(z,y,x): 30.68098471 128.9858818 128.9017075 > >> CoM_real(x,y,z): 2.09258826 70.06459185 43.54402081 > >> > >> Histogram: (null) > >> Total voxels: 3932160 > >> # voxels: 2178980 > >> % of total: 55.41432699 > >> Median: 0.1142372932 > >> Majority: 0.0002499721886 > >> BiModalT: 0.3392122686 > >> PctT [ 0%]: 0.0002499721886 > >> Entropy : 9.187178001 > >> > >> localhost[~/nrx/t2map]$ mincstats subject_t2map.mnc.gz -mask > >> subject_t2map_mask.mnc.gz -mask_binvalue 1.0 > >> File: subject_t2map.mnc.gz > >> Mask file: subject_t2map_mask.mnc.gz > >> Total voxels: 3932160 > >> # voxels: 1962553 > >> % of total: 49.91030375 > >> Volume (mm3): 5887659 > >> Min: 0.01020694431 > >> Max: 0.9998887777 > >> Sum: 415156.0653 > >> Sum^2: 161711.3365 > >> Mean: 0.211538779 > >> Variance: 0.0376498199 > >> Stddev: 0.194035615 > >> CoM_voxel(z,y,x): 30.68098471 128.9858818 128.9017075 > >> CoM_real(x,y,z): 2.09258826 70.06459185 43.54402081 > >> > >> Histogram: (null) > >> Total voxels: 3932160 > >> # voxels: 1962553 > >> % of total: 49.91030375 > >> Median: 0.1242361822 > >> Majority: 0.09273968637 > >> BiModalT: 0.3552104831 > >> PctT [ 0%]: 0.0002499721886 > >> Entropy : 9.681988728 > >> > >> > >> And here is the full mincheader: > >> localhost[~/nrx/t2map]$ mincheader subject_t2map.mnc.gz > >> netcdf mincheader-18621-tmp { > >> dimensions: > >> zspace = 60 ; > >> yspace = 256 ; > >> xspace = 256 ; > >> variables: > >> double zspace(zspace) ; > >> zspace:varid = "MINC standard variable" ; > >> zspace:vartype = "dimension____" ; > >> zspace:version = "MINC Version 1.0" ; > >> zspace:comments = "Z increases from patient inferior to superior" ; > >> zspace:spacing = "regular__" ; > >> zspace:alignment = "centre" ; > >> zspace:step = 3. ; > >> zspace:start = -53.5106888535874 ; > >> zspace:spacetype = "native____" ; > >> zspace:direction_cosines = 0.00888470442653803, -0.0702364344961855, > >> 0.997490804617524 ; > >> int yspace ; > >> yspace:varid = "MINC standard variable" ; > >> yspace:vartype = "dimension____" ; > >> yspace:version = "MINC Version 1.0" ; > >> yspace:comments = "Y increases from patient posterior to anterior" ; > >> yspace:spacing = "regular__" ; > >> yspace:alignment = "centre" ; > >> yspace:step = -1. ; > >> yspace:start = 201.955416409066 ; > >> yspace:spacetype = "native____" ; > >> yspace:direction_cosines = 0.0303997023189596, 0.997088076060185, > >> 0.0699373053349794 ; > >> int xspace ; > >> xspace:varid = "MINC standard variable" ; > >> xspace:vartype = "dimension____" ; > >> xspace:version = "MINC Version 1.0" ; > >> xspace:comments = "X increases from patient left to right" ; > >> xspace:spacing = "regular__" ; > >> xspace:alignment = "centre" ; > >> xspace:step = -1. ; > >> xspace:start = 128.433460913677 ; > >> xspace:spacetype = "native____" ; > >> xspace:direction_cosines = 0.999498332440992, -0.0297021098791549, > >> -0.0109940036566919 ; > >> double image-max(zspace) ; > >> image-max:varid = "MINC standard variable" ; > >> image-max:vartype = "var_attribute" ; > >> image-max:version = "MINC Version 1.0" ; > >> image-max:_FillValue = 1. ; > >> image-max:parent = "image" ; > >> double image-min(zspace) ; > >> image-min:varid = "MINC standard variable" ; > >> image-min:vartype = "var_attribute" ; > >> image-min:version = "MINC Version 1.0" ; > >> image-min:_FillValue = 0. ; > >> image-min:parent = "image" ; > >> float image(zspace, yspace, xspace) ; > >> image:parent = "rootvariable" ; > >> image:varid = "MINC standard variable" ; > >> image:vartype = "group________" ; > >> image:version = "MINC Version 1.0" ; > >> image:image-max = "--->image-max" ; > >> image:image-min = "--->image-min" ; > >> image:valid_range = 0.f, 0.9998888f ; > >> image:complete = "true_" ; > >> int rootvariable ; > >> rootvariable:varid = "MINC standard variable" ; > >> rootvariable:vartype = "group________" ; > >> rootvariable:version = "MINC Version 1.0" ; > >> rootvariable:parent = "" ; > >> rootvariable:children = "image" ; > >> > >> // global attributes: > >> :ident = "redacted" ; > >> :minc_version = "2.2.00" ; > >> :history = "Thu Jan 19 10:55:35 2017>>> mincmath -clobber -mult > >> subject_t2map_mask.mnc TMP6_t2map_unclamped.mnc subject_t2map.mnc\n", > >> "" ; > >> } > >> > >> > >> And here is my minc package info stuff: > >> localhost[~/nrx/t2map]$ which register > >> /opt/minc-toolkit/0.3.16/bin/register > >> > >> localhost[~/nrx/t2map]$ register -version > >> register: Version: 1.4.00 > >> > >> localhost[~/nrx/t2map]$ mincstats -version > >> program: 2.2.00 > >> libminc: 2.2.00 > >> netcdf : 4.2.1 of Feb 19 2015 15:50:30 $ > >> HDF5 : 1.8.8 > >> > >> localhost[~/nrx/t2map]$ cat /etc/system-release > >> CentOS release 6.5 (Final) > >> > >> localhost[~/nrx/t2map]$ uname -a > >> Linux localhost.localdomain 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 > >> 21:14:45 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > >> > >> Any come across this bug before? Any ideas on how to fix it so it is > >> viewable in register? > >> _______________________________________________ > >> 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 at bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From dbolar at nmr.mgh.harvard.edu Fri May 19 12:10:48 2017 From: dbolar at nmr.mgh.harvard.edu (Divya Bolar) Date: Fri, 19 May 2017 12:10:48 -0400 Subject: [MINC-users] mincbeast question Message-ID: <48FA50EF-13BD-471D-8E16-9DD61603C028@nmr.mgh.harvard.edu> Hi all! I have a pretty basic question re: mincbeast; I am just trying to input a minc file and get the brain extracted output (with the same resolution etc). I've tried various options, e.g.: mincbeast /opt/minc/share/beast-library-1.1 ./test.mnc test2.mnc and mincbeast -no_mask /opt/minc/share/beast-library-1.1 test_forMincbeast.mnc output.mnc and mincbeast -same_resolution /opt/minc/share/beast-library-1.1 test_forMincbeast.mnc output.mnc I always get the following error: ERROR! Mask dimension does not match image dimension! Any suggestions? Thanks so much! Div P.S. I have a small example data set (100K); can send personally, but I think is getting blocked by user list. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. From vladimir.fonov at gmail.com Fri May 19 12:13:41 2017 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Fri, 19 May 2017 12:13:41 -0400 Subject: [MINC-users] mincbeast question In-Reply-To: <48FA50EF-13BD-471D-8E16-9DD61603C028@nmr.mgh.harvard.edu> References: <48FA50EF-13BD-471D-8E16-9DD61603C028@nmr.mgh.harvard.edu> Message-ID: <3e28b8cd-bbfe-be8e-ca4f-7658f0a85308@gmail.com> Try: mincresample -nearest ./test.mnc -like /opt/minc/share/beast-library-1.1/intersection_mask.mnc test_beast.mnc and then mincbeast on test_beast.mnc On 2017-05-19 12:10 PM, Divya Bolar wrote: > Hi all! > > I have a pretty basic question re: mincbeast; I am just trying to input a minc file and get the brain extracted output (with the same resolution etc). > > I've tried various options, e.g.: > mincbeast /opt/minc/share/beast-library-1.1 ./test.mnc test2.mnc > and > mincbeast -no_mask /opt/minc/share/beast-library-1.1 test_forMincbeast.mnc output.mnc > and > mincbeast -same_resolution /opt/minc/share/beast-library-1.1 test_forMincbeast.mnc output.mnc > > I always get the following error: > ERROR! Mask dimension does not match image dimension! > > Any suggestions? > > Thanks so much! > Div > > P.S. I have a small example data set (100K); can send personally, but I think is getting blocked by user list. > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > _______________________________________________ > 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 mishkind at gmail.com Fri May 19 16:22:20 2017 From: mishkind at gmail.com (Mishkin Derakhshan) Date: Fri, 19 May 2017 10:22:20 -1000 Subject: [MINC-users] minc file is not visible in register but is visible in Display In-Reply-To: References: <01b1f15a-f71c-e209-7a68-1ff89350e0c9@gmail.com> Message-ID: Bert, I tried that command but it just spits out the usage. I'm guessing my version of register doesn't have that global. I grepped through the output of `strings register` and indeed I didn't find any variable named Volume_voxel_type. Vlad, mincresahpe as a short worked so that is probably the workaround we will use instead of getting everyone to install a new version of register at this point. thanks, mishkin On Thu, May 18, 2017 at 12:47 PM, Robert D. Vincent wrote: > Hi, > > Sorry, I replied to this earlier but used the wrong email address, so that > message is probably awaiting moderation. > > A more recent version of Register might help. Some versions can't deal with > float volumes in the range 0-1. Anything built off the current develop > branch should be fine. > > I'm not certain it will help with your version, but it might be useful to > try this: > > register -global Volume_voxel_type 0 subject_t2map.mnc.gz > > -bert > > On Thu, May 18, 2017 at 6:37 PM, Alex Zijdenbos > wrote: > > > Bert can probably be more specific, but there is a (more recent?) version > > of register that does the right thing on volumes like this. > > > > On Thu, May 18, 2017 at 4:02 PM, Vladimir S. FONOV < > > vladimir.fonov at gmail.com > > > wrote: > > > > > It's a bug in certain versions of register, affecting it's ability to > > show > > > files stored in float, with low values. > > > Can be fixed by mincreshape -short > > > > > > > > > > > > On 2017-05-18 03:47 PM, Mishkin Derakhshan wrote: > > > > > >> Hi, > > >> I have a file that when viewed in register is not viewable at all. It > is > > >> just blank (black) everywhere no matter what I do with the windowing. > > >> When I load it in Display it is just fine, so I know the data is > there. > > >> > > >> It is a systemic problem, i.e., all files that are created with my > > script > > >> have this problem of not being visible in register. > > >> > > >> I'm wondering if it has something to do with the range of my data > > because > > >> if I do further operations on it, then the downstream files load okay. > > >> > > >> For example, the file that currently does not load is > > subject_t2map.mnc.gz > > >> which contains float values from 0 to 1. > > >> > > >> If I do something like this, then the resulting 100.mnc loads just > fine > > in > > >> register: > > >> minccalc -expr 'A[0]*100' subject_t2map.mnc.gz 100.mnc > > >> > > >> Here are the mincstats of my file with/without a mask: > > >> > > >> localhost[~/nrx/t2map]$ mincstats subject_t2map.mnc.gz > > >> File: subject_t2map.mnc.gz > > >> Mask file: (null) > > >> Total voxels: 3932160 > > >> # voxels: 2178980 > > >> % of total: 55.41432699 > > >> Volume (mm3): 6536940 > > >> Min: 0 > > >> Max: 0.9998887777 > > >> Sum: 415156.0653 > > >> Sum^2: 161711.3365 > > >> Mean: 0.1905277081 > > >> Variance: 0.03791344611 > > >> Stddev: 0.1947137543 > > >> CoM_voxel(z,y,x): 30.68098471 128.9858818 128.9017075 > > >> CoM_real(x,y,z): 2.09258826 70.06459185 43.54402081 > > >> > > >> Histogram: (null) > > >> Total voxels: 3932160 > > >> # voxels: 2178980 > > >> % of total: 55.41432699 > > >> Median: 0.1142372932 > > >> Majority: 0.0002499721886 > > >> BiModalT: 0.3392122686 > > >> PctT [ 0%]: 0.0002499721886 > > >> Entropy : 9.187178001 > > >> > > >> localhost[~/nrx/t2map]$ mincstats subject_t2map.mnc.gz -mask > > >> subject_t2map_mask.mnc.gz -mask_binvalue 1.0 > > >> File: subject_t2map.mnc.gz > > >> Mask file: subject_t2map_mask.mnc.gz > > >> Total voxels: 3932160 > > >> # voxels: 1962553 > > >> % of total: 49.91030375 > > >> Volume (mm3): 5887659 > > >> Min: 0.01020694431 > > >> Max: 0.9998887777 > > >> Sum: 415156.0653 > > >> Sum^2: 161711.3365 > > >> Mean: 0.211538779 > > >> Variance: 0.0376498199 > > >> Stddev: 0.194035615 > > >> CoM_voxel(z,y,x): 30.68098471 128.9858818 128.9017075 > > >> CoM_real(x,y,z): 2.09258826 70.06459185 43.54402081 > > >> > > >> Histogram: (null) > > >> Total voxels: 3932160 > > >> # voxels: 1962553 > > >> % of total: 49.91030375 > > >> Median: 0.1242361822 > > >> Majority: 0.09273968637 > > >> BiModalT: 0.3552104831 > > >> PctT [ 0%]: 0.0002499721886 > > >> Entropy : 9.681988728 > > >> > > >> > > >> And here is the full mincheader: > > >> localhost[~/nrx/t2map]$ mincheader subject_t2map.mnc.gz > > >> netcdf mincheader-18621-tmp { > > >> dimensions: > > >> zspace = 60 ; > > >> yspace = 256 ; > > >> xspace = 256 ; > > >> variables: > > >> double zspace(zspace) ; > > >> zspace:varid = "MINC standard variable" ; > > >> zspace:vartype = "dimension____" ; > > >> zspace:version = "MINC Version 1.0" ; > > >> zspace:comments = "Z increases from patient inferior to superior" ; > > >> zspace:spacing = "regular__" ; > > >> zspace:alignment = "centre" ; > > >> zspace:step = 3. ; > > >> zspace:start = -53.5106888535874 ; > > >> zspace:spacetype = "native____" ; > > >> zspace:direction_cosines = 0.00888470442653803, -0.0702364344961855, > > >> 0.997490804617524 ; > > >> int yspace ; > > >> yspace:varid = "MINC standard variable" ; > > >> yspace:vartype = "dimension____" ; > > >> yspace:version = "MINC Version 1.0" ; > > >> yspace:comments = "Y increases from patient posterior to anterior" ; > > >> yspace:spacing = "regular__" ; > > >> yspace:alignment = "centre" ; > > >> yspace:step = -1. ; > > >> yspace:start = 201.955416409066 ; > > >> yspace:spacetype = "native____" ; > > >> yspace:direction_cosines = 0.0303997023189596, 0.997088076060185, > > >> 0.0699373053349794 ; > > >> int xspace ; > > >> xspace:varid = "MINC standard variable" ; > > >> xspace:vartype = "dimension____" ; > > >> xspace:version = "MINC Version 1.0" ; > > >> xspace:comments = "X increases from patient left to right" ; > > >> xspace:spacing = "regular__" ; > > >> xspace:alignment = "centre" ; > > >> xspace:step = -1. ; > > >> xspace:start = 128.433460913677 ; > > >> xspace:spacetype = "native____" ; > > >> xspace:direction_cosines = 0.999498332440992, -0.0297021098791549, > > >> -0.0109940036566919 ; > > >> double image-max(zspace) ; > > >> image-max:varid = "MINC standard variable" ; > > >> image-max:vartype = "var_attribute" ; > > >> image-max:version = "MINC Version 1.0" ; > > >> image-max:_FillValue = 1. ; > > >> image-max:parent = "image" ; > > >> double image-min(zspace) ; > > >> image-min:varid = "MINC standard variable" ; > > >> image-min:vartype = "var_attribute" ; > > >> image-min:version = "MINC Version 1.0" ; > > >> image-min:_FillValue = 0. ; > > >> image-min:parent = "image" ; > > >> float image(zspace, yspace, xspace) ; > > >> image:parent = "rootvariable" ; > > >> image:varid = "MINC standard variable" ; > > >> image:vartype = "group________" ; > > >> image:version = "MINC Version 1.0" ; > > >> image:image-max = "--->image-max" ; > > >> image:image-min = "--->image-min" ; > > >> image:valid_range = 0.f, 0.9998888f ; > > >> image:complete = "true_" ; > > >> int rootvariable ; > > >> rootvariable:varid = "MINC standard variable" ; > > >> rootvariable:vartype = "group________" ; > > >> rootvariable:version = "MINC Version 1.0" ; > > >> rootvariable:parent = "" ; > > >> rootvariable:children = "image" ; > > >> > > >> // global attributes: > > >> :ident = "redacted" ; > > >> :minc_version = "2.2.00" ; > > >> :history = "Thu Jan 19 10:55:35 2017>>> mincmath -clobber -mult > > >> subject_t2map_mask.mnc TMP6_t2map_unclamped.mnc subject_t2map.mnc\n", > > >> "" ; > > >> } > > >> > > >> > > >> And here is my minc package info stuff: > > >> localhost[~/nrx/t2map]$ which register > > >> /opt/minc-toolkit/0.3.16/bin/register > > >> > > >> localhost[~/nrx/t2map]$ register -version > > >> register: Version: 1.4.00 > > >> > > >> localhost[~/nrx/t2map]$ mincstats -version > > >> program: 2.2.00 > > >> libminc: 2.2.00 > > >> netcdf : 4.2.1 of Feb 19 2015 15:50:30 $ > > >> HDF5 : 1.8.8 > > >> > > >> localhost[~/nrx/t2map]$ cat /etc/system-release > > >> CentOS release 6.5 (Final) > > >> > > >> localhost[~/nrx/t2map]$ uname -a > > >> Linux localhost.localdomain 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun > 19 > > >> 21:14:45 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > > >> > > >> Any come across this bug before? Any ideas on how to fix it so it is > > >> viewable in register? > > >> _______________________________________________ > > >> 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 at bic.mni.mcgill.ca > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > > > > > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From dbolar at nmr.mgh.harvard.edu Fri May 19 11:49:24 2017 From: dbolar at nmr.mgh.harvard.edu (Divya Bolar) Date: Fri, 19 May 2017 11:49:24 -0400 Subject: [MINC-users] mincbeast question In-Reply-To: References: Message-ID: Hi all, I have a pretty basic question re: mincbeast; I am just trying to input a minc file and get the brain extracted output (with the same resolution etc). I've tried various options, e.g.: mincbeast /opt/minc/share/beast-library-1.1 ./test.mnc test2.mnc and mincbeast -no_mask /opt/minc/share/beast-library-1.1 test_forMincbeast.mnc output.mnc and mincbeast -same_resolution /opt/minc/share/beast-library-1.1 test_forMincbeast.mnc output.mnc I always get the following error: ERROR! Mask dimension does not match image dimension! Any suggestions? Thanks so much! Div The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. From eskild at gmail.com Mon May 22 08:10:03 2017 From: eskild at gmail.com (Simon Eskildsen) Date: Mon, 22 May 2017 14:10:03 +0200 Subject: [MINC-users] mincbeast question In-Reply-To: <48FA50EF-13BD-471D-8E16-9DD61603C028@nmr.mgh.harvard.edu> References: <48FA50EF-13BD-471D-8E16-9DD61603C028@nmr.mgh.harvard.edu> Message-ID: Did you run beast_normalize on your files before running mincbeast? You can find an excellent introduction to BEaST here: http://rstudio-pubs-static.s3.amazonaws.com/8431_d05daa5d49aa4cada417b6afc8ffd295.html Simon On Fri, May 19, 2017 at 6:10 PM, Divya Bolar wrote: > Hi all! > > I have a pretty basic question re: mincbeast; I am just trying to input a > minc file and get the brain extracted output (with the same resolution etc). > > I've tried various options, e.g.: > mincbeast /opt/minc/share/beast-library-1.1 ./test.mnc test2.mnc > and > mincbeast -no_mask /opt/minc/share/beast-library-1.1 > test_forMincbeast.mnc output.mnc > and > mincbeast -same_resolution /opt/minc/share/beast-library-1.1 > test_forMincbeast.mnc output.mnc > > I always get the following error: > ERROR! Mask dimension does not match image dimension! > > Any suggestions? > > Thanks so much! > Div > > P.S. I have a small example data set (100K); can send personally, but I > think is getting blocked by user list. > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From dbolar at nmr.mgh.harvard.edu Mon May 22 09:03:28 2017 From: dbolar at nmr.mgh.harvard.edu (Divya Bolar) Date: Mon, 22 May 2017 09:03:28 -0400 Subject: [MINC-users] mincbeast question In-Reply-To: References: <48FA50EF-13BD-471D-8E16-9DD61603C028@nmr.mgh.harvard.edu> Message-ID: <48E58C09-7571-43A6-B118-656AE01506A4@nmr.mgh.harvard.edu> Thank you Simon! Very useful, I did not see that! Div On May 22, 2017, at 8:10 AM, Simon Eskildsen wrote: > Did you run beast_normalize on your files before running mincbeast? > You can find an excellent introduction to BEaST here: > http://rstudio-pubs-static.s3.amazonaws.com/8431_d05daa5d49aa4cada417b6afc8ffd295.html > > Simon > > On Fri, May 19, 2017 at 6:10 PM, Divya Bolar > wrote: > >> Hi all! >> >> I have a pretty basic question re: mincbeast; I am just trying to input a >> minc file and get the brain extracted output (with the same resolution etc). >> >> I've tried various options, e.g.: >> mincbeast /opt/minc/share/beast-library-1.1 ./test.mnc test2.mnc >> and >> mincbeast -no_mask /opt/minc/share/beast-library-1.1 >> test_forMincbeast.mnc output.mnc >> and >> mincbeast -same_resolution /opt/minc/share/beast-library-1.1 >> test_forMincbeast.mnc output.mnc >> >> I always get the following error: >> ERROR! Mask dimension does not match image dimension! >> >> Any suggestions? >> >> Thanks so much! >> Div >> >> P.S. I have a small example data set (100K); can send personally, but I >> think is getting blocked by user list. >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >> > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > From dbolar at nmr.mgh.harvard.edu Mon May 22 09:04:05 2017 From: dbolar at nmr.mgh.harvard.edu (Divya Bolar) Date: Mon, 22 May 2017 09:04:05 -0400 Subject: [MINC-users] mincbeast question In-Reply-To: <3e28b8cd-bbfe-be8e-ca4f-7658f0a85308@gmail.com> References: <48FA50EF-13BD-471D-8E16-9DD61603C028@nmr.mgh.harvard.edu> <3e28b8cd-bbfe-be8e-ca4f-7658f0a85308@gmail.com> Message-ID: <830710FE-4A75-4798-BFE1-7D68BE299364@nmr.mgh.harvard.edu> Thanks Vladimir, I will try that! Div On May 19, 2017, at 12:13 PM, Vladimir S. FONOV wrote: > Try: > > mincresample -nearest ./test.mnc -like /opt/minc/share/beast-library-1.1/intersection_mask.mnc test_beast.mnc > > and then mincbeast on test_beast.mnc > > On 2017-05-19 12:10 PM, Divya Bolar wrote: >> Hi all! >> >> I have a pretty basic question re: mincbeast; I am just trying to input a minc file and get the brain extracted output (with the same resolution etc). >> >> I've tried various options, e.g.: >> mincbeast /opt/minc/share/beast-library-1.1 ./test.mnc test2.mnc >> and >> mincbeast -no_mask /opt/minc/share/beast-library-1.1 test_forMincbeast.mnc output.mnc >> and >> mincbeast -same_resolution /opt/minc/share/beast-library-1.1 test_forMincbeast.mnc output.mnc >> >> I always get the following error: >> ERROR! Mask dimension does not match image dimension! >> >> Any suggestions? >> >> Thanks so much! >> Div >> >> P.S. I have a small example data set (100K); can send personally, but I think is getting blocked by user list. >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in error >> but does not contain patient information, please contact the sender and properly >> dispose of the e-mail. >> _______________________________________________ >> 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 at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > From stebollmann at gmail.com Wed May 24 03:28:15 2017 From: stebollmann at gmail.com (Steffen Bollmann) Date: Wed, 24 May 2017 17:28:15 +1000 Subject: [MINC-users] undefined reference to `jpeg_mem_src' Message-ID: Hi all, I am trying to compile minc-toolkit-v2 develop and I get this error: [ 44%] Linking C executable dcm2mnc CMakeFiles/dcm2mnc.dir/dcm2mnc/dicom_read.c.o: In function `dicom_jpeg_decompress': dicom_read.c:(.text+0x4a4): undefined reference to `jpeg_mem_src' collect2: ld returned 1 exit status make[2]: *** [minctools/conversion/dcm2mnc] Error 1 make[1]: *** [minctools/conversion/CMakeFiles/dcm2mnc.dir/all] Error 2 make: *** [all] Error 2 How can I find out what is causing that error? Is it a missing library on the system where I build it? Could it be that libjpeg-dev is the culprit (guessing from 'jpeg_mem_src')? Thank you for any hints Steffen From bert at phalarope.com Wed May 24 06:16:50 2017 From: bert at phalarope.com (Robert D. Vincent) Date: Wed, 24 May 2017 06:16:50 -0400 Subject: [MINC-users] undefined reference to `jpeg_mem_src' In-Reply-To: References: Message-ID: You probably need to install a different version of libjpeg-dev I've been successfully building with libjpeg8-dev installed on a Ubuntu 16.04 system. -bert On Wed, May 24, 2017 at 3:28 AM, Steffen Bollmann wrote: > Hi all, > > I am trying to compile minc-toolkit-v2 develop and I get this error: > > [ 44%] Linking C executable dcm2mnc > CMakeFiles/dcm2mnc.dir/dcm2mnc/dicom_read.c.o: In function > `dicom_jpeg_decompress': > dicom_read.c:(.text+0x4a4): undefined reference to `jpeg_mem_src' > collect2: ld returned 1 exit status > make[2]: *** [minctools/conversion/dcm2mnc] Error 1 > make[1]: *** [minctools/conversion/CMakeFiles/dcm2mnc.dir/all] Error 2 > make: *** [all] Error 2 > > How can I find out what is causing that error? Is it a missing library on > the system where I build it? Could it be that libjpeg-dev is the culprit > (guessing from 'jpeg_mem_src')? > > Thank you for any hints > Steffen > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >