How to open DICOMs from a MR scan?

fiji
bio-formats
dicom

#1

Hi there,

I am trying to load a set of DICOM files. They are located in three different folders for organisation, and I need to stitch them together. Because they are compressed, I cannot use the default DICOM mechanism, and I am trying to use the Bio-Formats plugin to load all 3 (one folder = one DICOM Series).

After starting Bio-Formats from the plugin list, I select the first file from the first folder:

I then pick the option ‘Concatenate series when compatible’:

But then it acts as if there was only one file in the first Series:

For the curious, if I redo the experiment, but instead pick the first file from the second folder, it acts as if there was only a single file in the second folder this time:

What option should I select to read all files from all folders ?


#2

Hi Mathieu,

I can propose an indirect solution, decompress your DICOM first and open it with the regular DICOM reader of Fiji.
For Transcoding DICOMs I use DCM4CHE (dcm2dcm package).

Then you have Ilan’s Plugin called “Read From CD” which do a recurent scan of a DICOM directory and propose you available series.
See here : http://www.petctviewer.org/images/BI%20quick%20user%20guide1.pdf

Best regards,

Salim