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Fwd: Regarding Issue in reading binary files inside DICOM Directory

HBT hippocampal segmentation

Request regarding Lobular pooling

sudhakar Mishra

9 Nov 2019 9 Nov '19

11:03 p.m.

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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

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Selection_013.png (image/png — 14.0 KB)

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Tim Schäfer

10 Nov 10 Nov

4:09 a.m.

New subject: Fwd: Regarding Issue in reading binary files inside DICOM Directory

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Hi Sudhakar,

I'm sorry but I don't get the image. Especially not the part about kb and Mb. Is it supposed to mean that the file size in kb/MB is encoded in the file name?!

Could you maybe give the paths of 2 or 3 example image sets relative to the base dir of your study? Like:

<study>/<subject1>/S000XYZ.dcm?

If you have `tree` installed, this wwould also help:

cd <study> tree | head -n 50

Thanks,

Tim

On November 10, 2019 at 5:03 AM sudhakar Mishra rs163@iiita.ac.in wrote:
    External Email - Use Caution        
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

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Greve, Douglas N.,Ph.D.

11 Nov 11 Nov

12:26 p.m.

New subject: Fwd: Regarding Issue in reading binary files inside DICOM Directory

I have no idea what that image means. Have you tried using dcmunpack? You can pass it a folder and it should find all the dicoms in there

On 11/9/19 11:03 PM, sudhakar Mishra wrote:

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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

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sudhakar Mishra

17 Nov 17 Nov

11 a.m.

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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

Reply

Bruce Fischl

11:49 a.m.

New subject: Fwd: Regarding Issue in reading binary files inside DICOM Directory

sorry, I don't understand what your question is. What are you trying to do? Convert every dicom series in the directory? Convert a single series?

On Sun, 17 Nov 2019, sudhakar Mishra 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

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

Reply

Tim Schäfer

18 Nov 18 Nov

3:10 a.m.

New subject: 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:
    External Email - Use Caution        
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

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Bruce Fischl
Greve, Douglas N.,Ph.D.
sudhakar Mishra
Tim Schäfer