[MINC-users] dicom to minc converter
Andrew Janke
a.janke at gmail.com
Mon Nov 28 20:59:25 EST 2005
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
>
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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
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>
> ------------------------------
>
> 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
>
>
>
> ------------------------------
>
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--
Andrew Janke (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor)
Canada->Montreal Cell: +1 (514) 924 2012
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