Converting .dcm to COR files

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camilo＠nmr.mgh.harvard.edu

18 Aug 2006 18 Aug '06

5:32 p.m.

Hi Freesurfer help,

I am trying to convert my .dcm files to COR format. I use:

mri_convert -ot cor 003DCM 003

I get the following error:

mri_convert -ot cor 003DCM 003 reading from 003DCM... corRead(): can't open file /autofs/space/rao_001/users/patrickp/eeg_propofol/control_01... /bourget/control_01/mri/orig/003DCM/COR-.info

I am running the standar enviroment in the nmr, and the location of my files is: /autofs/space/rao_001/users/patrickp/eeg_propofol/control_01/... bourget/control_01/mri/orig

Can someone give me some advise in this issue?

Thanks,

Camilo

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Doug Greve

18 Aug 18 Aug

5:37 p.m.

Does the output directory exist and do you have permission to it?

btw, why are you using cor? We're trying to get people to stop :).

doug

camilo@nmr.mgh.harvard.edu wrote:

...

Hi Freesurfer help,

I am trying to convert my .dcm files to COR format. I use:

mri_convert -ot cor 003DCM 003

I get the following error:

mri_convert -ot cor 003DCM 003 reading from 003DCM... corRead(): can't open file /autofs/space/rao_001/users/patrickp/eeg_propofol/control_01... /bourget/control_01/mri/orig/003DCM/COR-.info

I am running the standar enviroment in the nmr, and the location of my files is: /autofs/space/rao_001/users/patrickp/eeg_propofol/control_01/... bourget/control_01/mri/orig

Can someone give me some advise in this issue?

Thanks,

Camilo

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Jenni Pacheco

5:38 p.m.

Hi Camilo,

You need to give it the path and filename for the first dicom in the series, I think 003DCM is the directory, so you'll need to include the file name for one of the dicoms.

Also, you should consider converting to a .mgz file - as that is the input for most everything that Freesurfer is doing these days, and not COR. To do this you can simply specify the output filename:

mri_convert /path/to/dicom/file.dcm /path/where/you/want/003.mgz

Jenni

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of camilo@nmr.mgh.harvard.edu Sent: Friday, August 18, 2006 5:33 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Converting .dcm to COR files

Hi Freesurfer help,

I am trying to convert my .dcm files to COR format. I use:

mri_convert -ot cor 003DCM 003

I get the following error:

mri_convert -ot cor 003DCM 003 reading from 003DCM... corRead(): can't open file /autofs/space/rao_001/users/patrickp/eeg_propofol/control_01... /bourget/control_01/mri/orig/003DCM/COR-.info

I am running the standar enviroment in the nmr, and the location of my files is: /autofs/space/rao_001/users/patrickp/eeg_propofol/control_01/... bourget/control_01/mri/orig

Can someone give me some advise in this issue?

Thanks,

Camilo

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Bruce Fischl

5:42 p.m.

do you mean 003.DCM? What is the name of the input volume? Is it dicom?

On Fri, 18 Aug 2006 camilo@nmr.mgh.harvard.edu wrote:

...

Hi Freesurfer help,

I am trying to convert my .dcm files to COR format. I use:

mri_convert -ot cor 003DCM 003

I get the following error:

mri_convert -ot cor 003DCM 003 reading from 003DCM... corRead(): can't open file /autofs/space/rao_001/users/patrickp/eeg_propofol/control_01... /bourget/control_01/mri/orig/003DCM/COR-.info

I am running the standar enviroment in the nmr, and the location of my files is: /autofs/space/rao_001/users/patrickp/eeg_propofol/control_01/... bourget/control_01/mri/orig

Can someone give me some advise in this issue?

Thanks,

Camilo

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Bruce Fischl
camilo＠nmr.mgh.harvard.edu
Doug Greve
Jenni Pacheco