Re: [Freesurfer] Fwd: Regarding Issue in reading binary files inside DICOM Directory

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We use the dcm2nii (or dcm2niix in the latest Linux version) from the MRICron software [1] to convert DICOMs to NIFTI format.

Install it and run like:

cd dir/with/dicoms /path/to/installed/dcm2nii <options> .

Note the dot (".") at the end of the command, which tells it to convert all files in the current directory.

You will have to adapt the <options> depending on what metadata from the DICOM headers you want dcm2nii to encode in the nifti file names. E.g,

/path/to/dcm2nii -i Y -g N -n Y .

Run /path/to/dcm2nii (without any options) to see all available options.

Best,

Tim

[1] https://www.nitrc.org/projects/mricron

On November 17, 2019 at 5:00 PM sudhakar Mishra rs163@iiita.ac.in wrote:

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Hi,

Sorry for the late reply. As I was asked the question about size. In reference to the query I am attaching the screenshot of terminal annotated with MB and KB for clarity. I am looking from your help.

Thanks, Sudhakar Mishra Research Scholar IIIT-Allahabad Website https://modelingemotion.wixsite.com/emotion

*सर्वद्वारेषु देहेऽस्मिन्प्रकाश उपजायते । ज्ञानं यदा तदा विद्याद्विवृद्धं सत्त्वमित्युत ॥* *तं विद्याद् दुःखसंयोगवियोगं योगसञ्ज्ञितम्। स निश्चयेन योक्तव्यो योगोऽनिर्विण्णचेतसा ||*

---------- Forwarded message --------- From: sudhakar Mishra rs163@iiita.ac.in Date: Sun, Nov 10, 2019 at 9:33 AM Subject: Fwd: Regarding Issue in reading binary files inside DICOM Directory To: freesurfer@nmr.mgh.harvard.edu, esr@thyrsus.com, < respond-auto@linuxmafia.com>

Hi,

I am facing problem in reading dicom files arranged in a way described in attached image.

I want to convert from this format to .nii format.

Please help me with this.

Thanks very much for considering my request

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

-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany