From jolinda at uoregon.edu  Thu Dec 29 12:17:42 2022
From: jolinda at uoregon.edu (Jolinda Smith)
Date: Thu, 29 Dec 2022 20:17:42 +0000
Subject: mriconvert: File does not contain image data
In-Reply-To: <PH0PR08MB65364427927232148503FCD480F39@PH0PR08MB6536.namprd08.prod.outlook.com>
References: <8C77467D58C51A44A747AA39660E13C39A138D@DAGONE.mdc-berlin.net>
 <8C77467D58C51A44A747AA39660E13C39A139D@DAGONE.mdc-berlin.net>
 <03de01d52786$d14ec900$73ec5b00$@uoregon.edu>
 <PH0PR08MB65364427927232148503FCD480F39@PH0PR08MB6536.namprd08.prod.outlook.com>
Message-ID: <SJ0PR10MB5423528A1FB601512350B6ADA0F39@SJ0PR10MB5423.namprd10.prod.outlook.com>

Hi Roman! Hope you are well.

This means that mcverter is reading it as DICOM, but it can't find the "photometric interpretation" tag (0028, 0004). For MR images this is usually "MONOCHROME2". If you have dcmtk installed, you can look for this tag by running dcmdump +P PhotometricInterpretation [filename]. If it's not found, mcverter assumes this isn't an image file.

I've mostly switched to dcm2niix myself since I haven't had time to work on mriconvert and it's gotten behind. I'm currently working on a python-based front end for dcm2niix that converts to bids format, if you are interested.

If you really want to use mcverter and not dcm2niix, the first thing I can think of to try is to rewrite the dicoms using something like dcmconv from dcmtk: https://support.dcmtk.org/docs/dcmconv.html. This should correct any missing required elements in the dicom files.

Jolinda

From: Roman Fleysher <roman.fleysher at einsteinmed.edu>
Sent: Thursday, December 29, 2022 11:55 AM
To: 'MRIConvert user's list' <mriconvert at lists.uoregon.edu>; Jolinda Smith <jolinda at uoregon.edu>
Subject: File does not contain image data

Dear Jolinda,
Dear All,

I have not had any issues with mcverter in a long time. I am installing a new system and new versions of software and some of the old DICOM files do not convert. New DICOMs are fine.

I get error message (when using -v option for verbose output):

Not added File does not contain image data

I use  mcverter version 2.1.0 build 434

The DICOM files are not that old, only few years, so this should not be any major change in format. What could this error mean and how to get mcverter to convert these DICOMs to NIFTI?

Thank you, and wishing you a Happy New Year,

Roman


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From jolinda at uoregon.edu  Thu Dec 29 13:19:49 2022
From: jolinda at uoregon.edu (Jolinda Smith)
Date: Thu, 29 Dec 2022 21:19:49 +0000
Subject: mriconvert: File does not contain image data
In-Reply-To: <PH0PR08MB65361264466D117FB53C149E80F39@PH0PR08MB6536.namprd08.prod.outlook.com>
References: <8C77467D58C51A44A747AA39660E13C39A138D@DAGONE.mdc-berlin.net>
 <8C77467D58C51A44A747AA39660E13C39A139D@DAGONE.mdc-berlin.net>
 <03de01d52786$d14ec900$73ec5b00$@uoregon.edu>
 <PH0PR08MB65364427927232148503FCD480F39@PH0PR08MB6536.namprd08.prod.outlook.com>
 <SJ0PR10MB5423528A1FB601512350B6ADA0F39@SJ0PR10MB5423.namprd10.prod.outlook.com>
 <PH0PR08MB65361264466D117FB53C149E80F39@PH0PR08MB6536.namprd08.prod.outlook.com>
Message-ID: <SJ0PR10MB5423B9E03BC3B96897D1D8A1A0F39@SJ0PR10MB5423.namprd10.prod.outlook.com>

At the point of the error it's just checking to see if the element is there. It might use it later to distinguish monochrome from RGB images but I'd have to dig through the code to be sure. I'm not sure if that would be needed for conversion, it might just be used for the image viewer in the gui. For images that are bright against a dark background (such as MR), MONOCHROME2 would be the correct value.

I have not used it, but gdcmtar (https://gdcm.sourceforge.net/html/gdcmtar.html) is supposed to convert to and from enhanced multiframe DICOM format.

Jolinda

From: Roman Fleysher <roman.fleysher at einsteinmed.edu>
Sent: Thursday, December 29, 2022 12:35 PM
To: Jolinda Smith <jolinda at uoregon.edu>; 'MRIConvert user's list' <mriconvert at lists.uoregon.edu>
Subject: Re: File does not contain image data

Thank you, Jolinda, for a quick reply !

In my experience, mcverter has always been superior to dcm2niix, and thus I try to stay with it. Yes, indeed, that tag is missing from the DICOM. I will try to insert it using dcmodify.

Does mcveter apply different conversion algorithm depending on value of PhotometricInterpretation? Or it simply uses it to differentiate images from non-images? (I thought there was another way to tell if DICOM has image, maybe SOPClassUID; I am not a DICOM expert.)

Since you mentioned a DICOM converter, do you know of a tool to assemble standard DICOM into an enhanced DICOM and disassemble enhanced into a standard?

Roman


________________________________
From: Jolinda Smith <jolinda at uoregon.edu<mailto:jolinda at uoregon.edu>>
Sent: Thursday, December 29, 2022 3:17 PM
To: Roman Fleysher <roman.fleysher at einsteinmed.edu<mailto:roman.fleysher at einsteinmed.edu>>; 'MRIConvert user's list' <mriconvert at lists.uoregon.edu<mailto:mriconvert at lists.uoregon.edu>>
Subject: RE: File does not contain image data

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Hi Roman! Hope you are well.



This means that mcverter is reading it as DICOM, but it can't find the "photometric interpretation" tag (0028, 0004). For MR images this is usually "MONOCHROME2". If you have dcmtk installed, you can look for this tag by running dcmdump +P PhotometricInterpretation [filename]. If it's not found, mcverter assumes this isn't an image file.



I've mostly switched to dcm2niix myself since I haven't had time to work on mriconvert and it's gotten behind. I'm currently working on a python-based front end for dcm2niix that converts to bids format, if you are interested.



If you really want to use mcverter and not dcm2niix, the first thing I can think of to try is to rewrite the dicoms using something like dcmconv from dcmtk: https://support.dcmtk.org/docs/dcmconv.html<https://urldefense.com/v3/__https:/nam04.safelinks.protection.outlook.com/?url=https*3A*2F*2Fsupport.dcmtk.org*2Fdocs*2Fdcmconv.html&data=05*7C01*7Croman.fleysher*40einsteinmed.edu*7C982e919dd9504dd04b5e08dae9d9bf09*7C9c01f0fd65e040c089a82dfd51e62025*7C0*7C0*7C638079418676494653*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000*7C*7C*7C&sdata=J1capOZFWfMWHdVcnNXJufNtM3SEbHO2GkUV4R42H2M*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUl!!C5qS4YX3!G8ThYyrUhiUGjY22yLdxiAhVwdraOwb0BC0wodPQUbdFkWAg29dv0ZXalSVadlU1jlc9zVudHoOgOVizBdZtQcQhyTPjkt14dQ$>. This should correct any missing required elements in the dicom files.



Jolinda



From: Roman Fleysher <roman.fleysher at einsteinmed.edu<mailto:roman.fleysher at einsteinmed.edu>>
Sent: Thursday, December 29, 2022 11:55 AM
To: 'MRIConvert user's list' <mriconvert at lists.uoregon.edu<mailto:mriconvert at lists.uoregon.edu>>; Jolinda Smith <jolinda at uoregon.edu<mailto:jolinda at uoregon.edu>>
Subject: File does not contain image data



Dear Jolinda,

Dear All,



I have not had any issues with mcverter in a long time. I am installing a new system and new versions of software and some of the old DICOM files do not convert. New DICOMs are fine.



I get error message (when using -v option for verbose output):



Not added File does not contain image data



I use  mcverter version 2.1.0 build 434



The DICOM files are not that old, only few years, so this should not be any major change in format. What could this error mean and how to get mcverter to convert these DICOMs to NIFTI?



Thank you, and wishing you a Happy New Year,



Roman




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