[MINC-users] dicom to minc converter
Robert VINCENT
bert at bic.mni.mcgill.ca
Mon Nov 28 21:58:18 EST 2005
Hi Teodor,
The code is written to skip over files it doesn't recognize as being
consistent with the first DICOM file it finds. This could be misbehaving
for some reason with your files. Is there any way you could send me a few
examples?
-bert
On Mon, 28 Nov 2005, Andrew Janke wrote:
> It would appear (from the error) that the files are not even dicom.
> Can they be opened with anything else? imageJ/Osirix?
>
>
> a
>
> On 28/11/05, Teodor Stanescu <teodorst at cancerboard.ab.ca> wrote:
> > Hi,
> >
> > I tried to convert some dicom images (Philips, Intera 3T) into mnc format using dcm2mnc and I got the following error:
> >
> > Checking file types...
> > File /home/teo/imags/1.3.46.670589.11.0.0.11.4.2.0.10138.5.5100.2004091311513190174.dcm appears to be DICOM (CD/Export).
> > Parsing 28 files |<--Skipping file /home/teo/imags/1.3.46.670589.11.0.0.11.4.2.0.10138.5.5100.2004091311513190174.dcm, which is not in theexpected format.
> > ->Skipping file /home/teo/imags/1.3.46.670589.11.0.0.11.4.2.0.10138.5.5100.2004091311513198175.dcm, which is not in the expected format.
> > -->Skipping file /home/teo/imags/1.3.46.670589.11.0.0.11.4.2.0.10138.5.5100.2004091311513204176.dcm, which is not in the expected format.
> > -->Skipping file /home/teo/imags/1.3.46.670589.11.0.0.11.4.2.0.10138.5.5100.2004091311513210177.dcm, which is not in the expected format.
> >
> > [...]
> >
> > Skipping file /home/teo/imags/1.3.46.670589.11.0.0.11.4.2.0.10138.5.5100.2004091311531998201.dcm, which is not in the expected format.
> > Sorting 0 files... Done sorting files.
> > Processing files, one series at a time...
> > Done processing files.
> >
> > Can anyone help me with some suggestions?
> > Thank you.
> >
> > Teo
> >
> >
> > -----Original Message-----
> > From: minc-users-bounces at bic.mni.mcgill.ca on behalf of minc-users-request at bic.mni.mcgill.ca
> > Sent: Fri 11/25/2005 10:00 AM
> > To: minc-users at bic.mni.mcgill.ca
> > Subject: MINC-users Digest, Vol 4, Issue 11
> >
> > Send MINC-users mailing list submissions to
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> >
> >
> > Today's Topics:
> >
> > 1. Re: MINC-users Digest, Vol 4, Issue 10 (Teodor Stanescu)
> > 2. Questions about MNI-Autoreg ((Jessie) Ting Guo)
> > 3. Re: Questions about MNI-Autoreg (Andrew Janke)
> > 4. Re: MINC-users Digest, Vol 4, Issue 10 (Andrew Janke)
> > 5. Re: Help on how to transform a displacement field!!!
> > (Andrew Janke)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Thu, 24 Nov 2005 12:56:43 -0700
> > From: "Teodor Stanescu" <teodorst at cancerboard.ab.ca>
> > Subject: Re: [MINC-users] MINC-users Digest, Vol 4, Issue 10
> > To: <minc-users at bic.mni.mcgill.ca>
> > Message-ID:
> > <86A652071AFE5548AA1C648AD489A15E012005C4 at ACBEXCHANGE.ad.cancerboard.ab.ca>
> >
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Hi Andrew,
> >
> > > The ./mritotal would make me think that in order to run mritotal you do this:
> > >
> > > cd /usr/local/mni/bin
> > > ./mritotal -help
> > >
> > > ?
> >
> > Yes, that is correct.
> >
> > > In this case I think the solution is simply that you need to add
> > > /usr/local/mni/bin to your PATH variable (in either your ~/.bashrc or
> > > ~/.cshrc).
> > >
> > > If you cd to your home directory and type this what happens?
> > >
> > > cd ~/
> > > which mritotal
> > > which mincresample
> >
> > Yes, by setting PATH=/usr/local/mni/bin:$PATH the initial problem with mritotal was fixed.
> > Now, I can still not run mritotal due to make_model. I was not able to build the model during make install process in mni_autoreg_model-1.03 directory.
> > If I run ./mritotal in.mnc out.xfm I would get the following error:
> >
> > Loading configuration file /usr/local/mni/bin/../etc/mni_autoreg/mritotal.cfg
> > Loading protocol default (protocol file = /usr/local/mni/bin/../etc/mni_autoreg/mritotal.default.cfg)
> > /usr/local/mni/bin/../share/mni_autoreg/average_305_16_blur.mnc does not exist
> > /usr/local/mni/bin/../share/mni_autoreg/average_305_8_blur.mnc does not exist
> > /usr/local/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc does not exist
> > /usr/local/mni/bin/../share/mni_autoreg/average_305_16_mask.mnc does not exist
> > /usr/local/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc does not exist
> >
> > In /usr/local/mni/share/mni_autoreg there are only 3 files:
> > average_305_headmask.mnc
> > average_305_mask.mnc
> > average_305.mnc.
> >
> > Thank you for your help.
> >
> > Teo
> >
> >
> > This e-mail and any attachments may contain confidential and
> > privileged information. If you are not the intended recipient,
> > please notify the sender immediately by return e-mail, delete this
> > e-mail and destroy any copies. Any dissemination or use of this
> > information by a person other than the intended recipient is
> > unauthorized and may be illegal.
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Thu, 24 Nov 2005 15:15:13 -0500
> > From: "\(Jessie\) Ting Guo" <tguo at imaging.robarts.ca>
> > Subject: [MINC-users] Questions about MNI-Autoreg
> > To: <minc-users at bic.mni.mcgill.ca>
> > Message-ID: <006701c5f133$d34d93f0$c32914c6 at irus.robarts.ca>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Hello everyone,
> >
> > I have a few questions regarding the MNI Autoreg.
> >
> > 1. Does anyone know where I can find the latest version of MNI Autoreg? Is the one on http://www.bic.mni.mcgill.ca/software/distribution/ the latest version?
> >
> > 2. Is this version based on optical flow or intensity-based cross correlation? I want to use intensity-based corss correlation. Where can I find that?
> >
> > 3. If I change the target image from mni_305.mnc to sbrain.mnc, will that significantly affect the registration accuracy?
> >
> > Thanks a lot!
> >
> > Jessie
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Thu, 24 Nov 2005 20:40:32 -0500
> > From: Andrew Janke <a.janke at gmail.com>
> > Subject: Re: [MINC-users] Questions about MNI-Autoreg
> > To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> > Message-ID: <d747ed50511241740n16ac6173k at mail.gmail.com>
> > Content-Type: text/plain; charset=ISO-8859-1
> >
> > > I have a few questions regarding the MNI Autoreg.
> > >
> > > 1. Does anyone know where I can find the latest version of MNI Autoreg? Is the one on http://www.bic.mni.mcgill.ca/software/distribution/ the latest version?
> >
> > packages.bic.mni.mcgill.ca/tgz
> >
> > > 2. Is this version based on optical flow or intensity-based cross correlation? I want to use intensity-based corss correlation. Where can I find that?
> >
> > Intensity cross correlation by default.
> >
> > > 3. If I change the target image from mni_305.mnc to sbrain.mnc, will that significantly affect the registration accuracy?
> >
> > sbrain? I'm afraid you lost me.. :)
> >
> >
> > --
> > Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor)
> > Canada->Montreal Cell: +1 (514) 924 2012
> >
> >
> >
> > ------------------------------
> >
> > Message: 4
> > Date: Thu, 24 Nov 2005 20:43:23 -0500
> > From: Andrew Janke <a.janke at gmail.com>
> > Subject: Re: [MINC-users] MINC-users Digest, Vol 4, Issue 10
> > To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> > Message-ID: <d747ed50511241743m19cd20b7p at mail.gmail.com>
> > Content-Type: text/plain; charset=ISO-8859-1
> >
> > > Now, I can still not run mritotal due to make_model. I was not able to build the model during make install process in mni_autoreg_model-1.03 directory.
> >
> > What was the error in the install process? Looks to me (from the
> > below) that the install didn't complete and only files were copied. i
> > suspect again this is because make_model (part of the mni_autoreg
> > install) was not on your path when you installed the model files
> > package.
> >
> > > If I run ./mritotal in.mnc out.xfm I would get the following error:
> > >
> > > Loading configuration file /usr/local/mni/bin/../etc/mni_autoreg/mritotal.cfg
> > > Loading protocol default (protocol file = /usr/local/mni/bin/../etc/mni_autoreg/mritotal.default.cfg)
> > > /usr/local/mni/bin/../share/mni_autoreg/average_305_16_blur.mnc does not exist
> > > /usr/local/mni/bin/../share/mni_autoreg/average_305_8_blur.mnc does not exist
> > > /usr/local/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc does not exist
> > > /usr/local/mni/bin/../share/mni_autoreg/average_305_16_mask.mnc does not exist
> > > /usr/local/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc does not exist
> > >
> > > In /usr/local/mni/share/mni_autoreg there are only 3 files:
> > > average_305_headmask.mnc
> > > average_305_mask.mnc
> > > average_305.mnc.
> >
> > So, now that you have fixed your path you can either re-install the
> > model files or do this:
> >
> > cd /usr/loca/mni/share/mni_autoreg
> > make_model average_305
> >
> > --
> > Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor)
> > Canada->Montreal Cell: +1 (514) 924 2012
> >
> >
> >
> > ------------------------------
> >
> > Message: 5
> > Date: Thu, 24 Nov 2005 22:40:25 -0500
> > From: Andrew Janke <a.janke at gmail.com>
> > Subject: Re: [MINC-users] Help on how to transform a displacement
> > field!!!
> > To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> > Message-ID: <d747ed50511241940w2fe2e238v at mail.gmail.com>
> > Content-Type: text/plain; charset=ISO-8859-1
> >
> > > I would like to understand what "a non-mass
> > > preserving resampling" means.
> >
> > It is the notion of preserving signal as it relates to area in the
> > original image. ie: if you shrink an area by 10% you increase its
> > signal by 10%. Thus if you integrate across an area both before and
> > after resampling you will get the same result. Sometimes you want to
> > do this and sometimes you dont.....
> >
> > > Does this mean that I won't be able to apply mincblob on the results?
> >
> > no
> >
> > > Maybe, it would be better to decompose the vectors at each voxel of the deformation and resample that instead. The only problem is to reassemble the vector field.
> >
> > why? This is in effect what mincresample does.
> >
> >
> > --
> > Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor)
> > Canada->Montreal Cell: +1 (514) 924 2012
> >
> >
> >
> > ------------------------------
> >
> > _______________________________________________
> > 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 4, Issue 11
> > *****************************************
> >
> >
> >
> > This e-mail and any attachments may contain confidential and
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> > please notify the sender immediately by return e-mail, delete this
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> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> >
> >
>
>
> --
> Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor)
> Canada->Montreal Cell: +1 (514) 924 2012
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
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