cerr / CERR

Matlab/Octave based platform for Radiological Research.
https://cerr.github.io/CERR/
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Cannot import DICOM #677

Open sterparia opened 2 years ago

sterparia commented 2 years ago

Hi there, I've recently upgraded to Matlab 2021b and I'm having issues importing DICOM data.

CERR CERR>> Scanning DICOM directory Reading directory:C:\Users\sami_\Desktop\Prostate vsmall bladder ... Reading header ... CERR>> DICOM Import has no methods defined for import into the planC{indexS.header}.sponsorID field, leaving empty. CERR>> DICOM Import has no methods defined for import into the planC{indexS.header}.protocolID field, leaving empty. CERR>> DICOM Import has no methods defined for import into the planC{indexS.header}.subjectID field, leaving empty. CERR>> DICOM Import has no methods defined for import into the planC{indexS.header}.submissionID field, leaving empty. CERR>> DICOM Import has no methods defined for import into the planC{indexS.header}.timeSaved field, leaving empty. CERR>> DICOM Import has no methods defined for import into the planC{indexS.header}.lastSavedInVer field, leaving empty. CERR>> DICOM Import has no methods defined for import into the planC{indexS.header}.CERRImportVersion field, leaving empty. CERR>> DICOM Import has no methods defined for import into the planC{indexS.header}.anonymizedID field, leaving empty. Reading comment ... Reading scan ... Loading Scan ... Array indices must be positive integers or logical values.

Error in populate_planC_field (line 139) scanOriS(scansAdded).scanUID = dataS(scansAdded).scanUID;

Error in dcmdir2planC (line 53) cellData = populate_planC_field(cellNames{i}, dcmdir_PATIENT, optS);

Error in CERRImportDCM4CHE (line 120) planC = dcmdir2planC(combinedDcmdirS,mergeScansFlag,optS);

Error in CERR (line 133) CERRImportDCM4CHE;

Error while evaluating UIControl Callback.

Could someone please give me a hand with this? I saw a previous issue that said there may be an issue with whitespace? But not sure if it is the same problem here. Thanks. Sami

adityaapte commented 2 years ago

The error seems to result while importing the scan. Could you try removing the whitespace and see if that works?

On Fri, Jan 7, 2022, 5:04 AM sterparia @.***> wrote:

Hi there, I've recently upgraded to Matlab 2021b and I'm having issues importing DICOM data.

CERR CERR>> Scanning DICOM directory Reading directory:C:\Users\sami_\Desktop\Prostate vsmall bladder ... Reading header ... CERR>> DICOM Import has no methods defined for import into the planC{indexS.header}.sponsorID field, leaving empty. CERR>> DICOM Import has no methods defined for import into the planC{indexS.header}.protocolID field, leaving empty. CERR>> DICOM Import has no methods defined for import into the planC{indexS.header}.subjectID field, leaving empty. CERR>> DICOM Import has no methods defined for import into the planC{indexS.header}.submissionID field, leaving empty. CERR>> DICOM Import has no methods defined for import into the planC{indexS.header}.timeSaved field, leaving empty. CERR>> DICOM Import has no methods defined for import into the planC{indexS.header}.lastSavedInVer field, leaving empty. CERR>> DICOM Import has no methods defined for import into the planC{indexS.header}.CERRImportVersion field, leaving empty. CERR>> DICOM Import has no methods defined for import into the planC{indexS.header}.anonymizedID field, leaving empty. Reading comment ... Reading scan ... Loading Scan ... Array indices must be positive integers or logical values.

Error in populate_planC_field (line 139) scanOriS(scansAdded).scanUID = dataS(scansAdded).scanUID;

Error in dcmdir2planC (line 53) cellData = populate_planC_field(cellNames{i}, dcmdir_PATIENT, optS);

Error in CERRImportDCM4CHE (line 120) planC = dcmdir2planC(combinedDcmdirS,mergeScansFlag,optS);

Error in CERR (line 133) CERRImportDCM4CHE;

Error while evaluating UIControl Callback.

Could someone please give me a hand with this? I saw a previous issue that said there may be an issue with whitespace? But not sure if it is the same problem here. Thanks. Sami

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sterparia commented 2 years ago

Hi Aditya,

I've just tried to remove the whitespace in each of the above scripts but I'm still getting the same message :(

adityaapte commented 2 years ago

Any chance you can share anonymized data?

On Fri, Jan 7, 2022, 6:01 AM sterparia @.***> wrote:

Hi Aditya,

I've just tried to remove the whitespace in each of the above scripts but I'm still getting the same message :(

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sterparia commented 2 years ago

Ah.. do you think it could be an issue with a DICOM header and how I might have anonymised the data? I think that should be ok. Should I send it via email? Thanks!

adityaapte commented 2 years ago

I will send you a link to upload the data. Can you please let me know your email address for the link.

On Fri, Jan 7, 2022, 8:40 AM sterparia @.***> wrote:

Ah.. do you think it could be an issue with a DICOM header and how I might have anonymised the data? I think that should be ok. Should I send it via email? Thanks!

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sterparia commented 2 years ago

sami_kaur@hotmail.com

thanks!

ojalaj commented 1 year ago

@adityaapte @aditiiyer I got this same error with most recent version of CERR and Matlab R2022a on Linux 64-bit. I haven't experienced this error with earlier releases of CERR/Matlab, i.e., I'm trying to import a plan exported from TPS (CT, RP, RD, RS) that has been imported without any errors in the past (e.g. with CERR release from 26.2.2021 and Matlab R2015).

Any ideas what has happened since then and how to fix this?

adityaapte commented 1 year ago

Can you please post the error message? Thanks.

On Tue, Feb 7, 2023 at 8:23 AM ojalaj @.***> wrote:

@adityaapte https://github.com/adityaapte @aditiiyer https://github.com/aditiiyer I got this same error with most recent version of CERR and Matlab R2022a on Linux 64-bit. I haven't experienced this error with earlier releases of CERR/Matlab, i.e., I'm trying to import a plan exported from TPS (CT, RP, RD, RS) that has been imported without any errors in the past (e.g. with CERR release from 26.2.2021 and Matlab R2015).

Any ideas what has happened since then and how to fix this?

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