questions > No error shooting and No result
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Jan 10, 2023 08:01 PM | aoooooooo
No error shooting and No result
Dear Doc,
I successfully run the dic to Nifti once before with the same PC from IMA files to uncompressed Nifti. However, when I try to do it again with same files but compressed to nii.gz, the dcm2nii gave no result at all and also not error raised. I tried to delete and redownload, restart the pc. None of them worked. If you have any idea of what's wrong about my doing or suggestions to fix it please tell me.
Best wishes,
I successfully run the dic to Nifti once before with the same PC from IMA files to uncompressed Nifti. However, when I try to do it again with same files but compressed to nii.gz, the dcm2nii gave no result at all and also not error raised. I tried to delete and redownload, restart the pc. None of them worked. If you have any idea of what's wrong about my doing or suggestions to fix it please tell me.
Best wishes,
Jan 10, 2023 08:01 PM | Chris Rorden
RE: No error shooting and No result
1. Can you report the full output of running dcm2niix
2. The complete output reports the version in the first line of output:
Chris Rorden's dcm2niiX version v1.0.20220720 Clang12.0.5 ARM (64-bit MacOS)
If you are using a version prior to v1.0.20220720, does upgrading resolve your issue?
https://github.com/rordenlab/dcm2niix/releases/tag/v1.0.20220720
You can get the latest stable version from NITRC or Github
https://github.com/rordenlab/dcm2niix/releases
2. The complete output reports the version in the first line of output:
Chris Rorden's dcm2niiX version v1.0.20220720 Clang12.0.5 ARM (64-bit MacOS)
If you are using a version prior to v1.0.20220720, does upgrading resolve your issue?
https://github.com/rordenlab/dcm2niix/releases/tag/v1.0.20220720
You can get the latest stable version from NITRC or Github
https://github.com/rordenlab/dcm2niix/releases
Jan 11, 2023 01:01 PM | aoooooooo
RE: No error shooting and No result
Originally posted by Chris Rorden:
Compression will be faster with pigz.exe in the same folder as the executable
Chris Rorden's dcm2niiX version v1.0.20190902 (JP2:OpenJPEG) (JP-LS:CharLS) MSC1900 (64-bit Windows)
1. Can you report the full output of running
dcm2niix
2. The complete output reports the version in the first line of output:
Chris Rorden's dcm2niiX version v1.0.20220720 Clang12.0.5 ARM (64-bit MacOS)
If you are using a version prior to v1.0.20220720, does upgrading resolve your issue?
https://github.com/rordenlab/dcm2niix/releases/tag/v1.0.20220720
You can get the latest stable version from NITRC or Github
https://github.com/rordenlab/dcm2niix/releases
Thank you for your fast reply, here is
the out: F:\2023\BrainTools\MRIcron\Resources\dcm2niix.exe -f
"%f_%p_%t_%s" -p y -z y "F:\2023\1.project\tic
rating\fMRI\E01Pre"2. The complete output reports the version in the first line of output:
Chris Rorden's dcm2niiX version v1.0.20220720 Clang12.0.5 ARM (64-bit MacOS)
If you are using a version prior to v1.0.20220720, does upgrading resolve your issue?
https://github.com/rordenlab/dcm2niix/releases/tag/v1.0.20220720
You can get the latest stable version from NITRC or Github
https://github.com/rordenlab/dcm2niix/releases
Compression will be faster with pigz.exe in the same folder as the executable
Chris Rorden's dcm2niiX version v1.0.20190902 (JP2:OpenJPEG) (JP-LS:CharLS) MSC1900 (64-bit Windows)
Jan 11, 2023 03:01 PM | Chris Rorden
RE: No error shooting and No result
1. If you are using a version prior to v1.0.20220720, does
upgrading resolve your issue?
https://github.com/rordenlab/dcm2niix/re...
2. Does removing spaces in the file path change the behavior?
3. Is that really the complete text output, usually there is a warning if no files were found?
dcm2niix c:\empty
Chris Rorden's dcm2niiX version v1.0.20220720 Clang12.0.5 ARM (64-bit MacOS)
Error: Unable to find any DICOM images in c:\empty (or subfolders 5 deep)
https://github.com/rordenlab/dcm2niix/re...
2. Does removing spaces in the file path change the behavior?
3. Is that really the complete text output, usually there is a warning if no files were found?
dcm2niix c:\empty
Chris Rorden's dcm2niiX version v1.0.20220720 Clang12.0.5 ARM (64-bit MacOS)
Error: Unable to find any DICOM images in c:\empty (or subfolders 5 deep)
Jan 11, 2023 03:01 PM | aoooooooo
RE: No error shooting and No result
Hi Chris,
Yes, I just re-confirmed that I'm using the new downloaded latest version.
Removing the space does not help, I once succedd tramsformed my IMA files to nii, but this time when I do the exactly same thing for nii.gz, it's not responding, the only reaction is: after several seconds pause, it shows:
F:\2023\BrainTools\MRIcron\Resources\dcm2niix.exe -f "%f_%p_%t_%s" -p y -z y "F:\2023\1.Project\tic_rating\fMRI\E01Pre"
Compression will be faster with pigz.exe in the same folder as the executable
Chris Rorden's dcm2niiX version v1.0.20220720 (JP2:OpenJPEG) (JP-LS:CharLS) MSC1900 (64-bit Windows)
on the right side of GUI screen.
And this time I changed tic rating to tic_rating, there is still nothing converted.
Best wishes,
Ao
Yes, I just re-confirmed that I'm using the new downloaded latest version.
Removing the space does not help, I once succedd tramsformed my IMA files to nii, but this time when I do the exactly same thing for nii.gz, it's not responding, the only reaction is: after several seconds pause, it shows:
F:\2023\BrainTools\MRIcron\Resources\dcm2niix.exe -f "%f_%p_%t_%s" -p y -z y "F:\2023\1.Project\tic_rating\fMRI\E01Pre"
Compression will be faster with pigz.exe in the same folder as the executable
Chris Rorden's dcm2niiX version v1.0.20220720 (JP2:OpenJPEG) (JP-LS:CharLS) MSC1900 (64-bit Windows)
on the right side of GUI screen.
And this time I changed tic rating to tic_rating, there is still nothing converted.
Best wishes,
Ao
Jan 11, 2023 03:01 PM | Chris Rorden
RE: No error shooting and No result
1. Instead of using the graphical interface, run the command
directly from the terminal.
2. Try running from the terminal without extra options, from the folder with the executable:
dcm2niix c:\path\to\DICOMs
3. Since you are not using the output folder option (`-o c:\path\to\NIfTI`) you need to make sure you have read write permission to the folder with the DICOMs, e.g. the F drive can not be a CD-ROM drive.
4. While I am happy my legacy tools have proved popular and are mature, I have a heavy teaching service and research burden. I do not actively maintain MRIcron, and have put my efforts into MRIcroGL (and am moving to NiiVue). Therefore, I would recommend you try out MRIcroGL which is designed to leverage modern hardware and operating systems.
https://github.com/rordenlab/MRIcroGL/releases
2. Try running from the terminal without extra options, from the folder with the executable:
dcm2niix c:\path\to\DICOMs
3. Since you are not using the output folder option (`-o c:\path\to\NIfTI`) you need to make sure you have read write permission to the folder with the DICOMs, e.g. the F drive can not be a CD-ROM drive.
4. While I am happy my legacy tools have proved popular and are mature, I have a heavy teaching service and research burden. I do not actively maintain MRIcron, and have put my efforts into MRIcroGL (and am moving to NiiVue). Therefore, I would recommend you try out MRIcroGL which is designed to leverage modern hardware and operating systems.
https://github.com/rordenlab/MRIcroGL/releases
Jan 12, 2023 02:01 PM | aoooooooo
RE: No error shooting and No result
Thank you for your patience,
I used the terminal, and finally find the error:
Error: Unable to find any DICOM images in F:\Study\1.2023\tic_rating\fMRI\E01Pre (or subfolders 5 deep).
The files were in IMA format, not DICOM, is there any way I can do this?
Best wishes,
Ao
I used the terminal, and finally find the error:
Error: Unable to find any DICOM images in F:\Study\1.2023\tic_rating\fMRI\E01Pre (or subfolders 5 deep).
The files were in IMA format, not DICOM, is there any way I can do this?
Best wishes,
Ao
Jan 12, 2023 03:01 PM | Chris Rorden
RE: No error shooting and No result
Feel free to share datasets with my institutional email for further
feedback
https://sc.edu/study/colleges_schools/artsandsciences/psychology/our_people/directory/rorden_chris.php
However, dcm2niix is designed to handle the very complex DICOM format, not other formats. While Some modern Siemens scanners use the file extension '.ima' for DICOM fragments (e.g. DICOM meta data without the Part 10 DICOM preamble), the .ima extension was also used for proprietary formats that pre-date the DICOM format
https://www.dclunie.com/medical-image-faq/html/part4.html
You may want to look at the provenance of your images, and see if you can export them as archival quality DICOM data.
https://sc.edu/study/colleges_schools/artsandsciences/psychology/our_people/directory/rorden_chris.php
However, dcm2niix is designed to handle the very complex DICOM format, not other formats. While Some modern Siemens scanners use the file extension '.ima' for DICOM fragments (e.g. DICOM meta data without the Part 10 DICOM preamble), the .ima extension was also used for proprietary formats that pre-date the DICOM format
https://www.dclunie.com/medical-image-faq/html/part4.html
You may want to look at the provenance of your images, and see if you can export them as archival quality DICOM data.