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Laura Costello
Mar 12, 2018, 5:55:37 AM3/12/18
to ExploreDTI
Hi,
I am trying to do the dicom to nifti conversion in ExploreDti v4.8.6 (run through matlab) using the plugin in plugins>convert>dicom folders to .nii files. The popup to use Chris Riordan's tool comes up but once I hit ok then I do not get the option to do the dicom to nifti conversion. Is there any reason this may be? Could it be that the matlab version of ExploreDTI missing this plugin? I have tried this using the standalone version of ExploreDTI v4.8.6 and I am able to convert files without any problems.
Thanks,
Laura
stijn m
Mar 22, 2018, 11:47:06 AM3/22/18
to ExploreDTI
Dear Laura,
Indeed the message comes up to use the tool from Chris Rorden (see http://people.cas.sc.edu/rorden/mricron/dcm2nii.html). This requires to install some extra tools to do the dicom to nifti conversion, before starting the analyses in ExploreDTI. There are also tools available to perform this conversion within Matlab (see https://nl.mathworks.com/matlabcentral/fileexchange/42997-dicom-to-nifti-converter--nifti-tool-and-viewer).
The big issue is that raw data from the MRI scanner can vary between scanner manufacturers. Most commonly dicoms are used, but some use par/rec files. Interestingly, some "standard" conversion tools are custom made and embedded in ExploreDTI. It would be a useful feature to have a dicom to nifti conversion for general use in ExploreDTI. But I guess this is not feasible at this point. Make sure when the conversion has been done, to check the orientation!
Related to this step before working in ExploreDTI is that you have to make sure the provided nifti files are unzipped. It would be great to have standard .nii.gz input and output from ExploreDTI dramatically reducing the file sizes.
HTH.
BW.
Stijn
Indeed the message comes up to use the tool from Chris Rorden (see http://people.cas.sc.edu/rorden/mricron/dcm2nii.html). This requires to install some extra tools to do the dicom to nifti conversion, before starting the analyses in ExploreDTI. There are also tools available to perform this conversion within Matlab (see https://nl.mathworks.com/matlabcentral/fileexchange/42997-dicom-to-nifti-converter--nifti-tool-and-viewer).
The big issue is that raw data from the MRI scanner can vary between scanner manufacturers. Most commonly dicoms are used, but some use par/rec files. Interestingly, some "standard" conversion tools are custom made and embedded in ExploreDTI. It would be a useful feature to have a dicom to nifti conversion for general use in ExploreDTI. But I guess this is not feasible at this point. Make sure when the conversion has been done, to check the orientation!
Related to this step before working in ExploreDTI is that you have to make sure the provided nifti files are unzipped. It would be great to have standard .nii.gz input and output from ExploreDTI dramatically reducing the file sizes.
HTH.
BW.
Stijn
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