Error in CoREgister using GE dicom folder

MRS Software Osprey
#1

Hi,

I am a PhD student just starting my first tries with Osprey, and have run into some trouble with GE dicom files.

When running CoRegister I get the following error:

Unrecognized function or variable ‘dcm_folder’.

Error in OspreyCoreg (line 145)
[vol_mask, T1_max, vol_image, voxel_ctr] = coreg_p(MRSCont.raw{kk}, dcm_folder,
maskFile);

Error in osp_onCoreg (line 45)
MRSCont = OspreyCoreg(MRSCont);

Error while evaluating UIControl Callback.

To get the whole folder path into the job file, I altered it manually, as it seems that I can only choose single files through the GUI.

I have tried shortening and changing the path, and verified that there are only .dcm files in the folder, without any luck.

All help is much appreciated :slight_smile:

Thanks!
Vera

#2

Hi Vera,

Can you post your job file here so we can take a look?

An alternative that should work out is to manually convert the DICOM data to NIfTI with SPM, dcm2niix or (my recommendation) dicm2nii which is actually included in the Osprey libraries. You can then supply the NIfTI files in the job file instead of pointing to the DICOM folder. The conversion is a useful step that you will likely do eventually anyway.

Thanks,
Georg

#3

Thanks for your super fast reply! Here’s the job file:
Job_test_dcm.pdf (19.4 KB)

Vera

#4

Hi Vera,

Thanks for the report. I’ve pushed a change to the develop branch in the Osprey GitHub repository. Please pull the latest changes from there and try again with the job file changed as described below:

The strrep(which( bits in the job files is really only there to make sure that the example data in the GitHub repository work out of the box for everyone; however, they seem to really confuse people more than help. I should look into finding a better way to solve this.

Please change

files_nii = {strrep(which('/Users/ver003/Projects/test_osprey_dcm/Subject_01/217/DICOM/1.dcm'),'1.dcm','')};

to

files_nii = {'/Users/ver003/Projects/test_osprey_dcm/Subject_01/217/DICOM/'};

and try again.

(The other change that you need to make is

editTarget = {'none'};

since you are using un-edited data.)

Let me know how it goes.

Best,
Georg

#5

Hi Georg,
Working now, thanks for excellent help!

Vera

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