Problem with conversion of EPI/T1 DICOM to NIFTI

Submitted by David on
Hi,
 
when I'm trying to convert EPI and T1 DICOMS to nifti, DPABI gets stuck in between. That is, it converts some data but then it just runs and runs without error message but not data is being converted anymore. For example I have raw dcm data from 30 test subjects I want to convert. DPABI starts and converts lets say 27 of the subjects EPI data, but it then goes on and on without converting more data and the T1 data conversion does not even start. I tried it with an older version of DPABI as well as with the latest version (V2.0_151201). I also tried it on two different computers and I'm using parallel processing. Up til now it was no problem and suddenly it doesn't work anymore. 
 
I tried it on a different dataset as well. There it is able to finish EPI/T1 conversion, but it only seems to convert 27 out of 30 EPI DICOMS and only 8 of 30 T1 DICOM (???).  
 
Any help or ideas how to find out what problem is appreciated.

YAN Chao-Gan

Thu, 01/07/2016 - 02:15

Permalink

Hi David,

What's the operation system are you using?

Could you try to turn off the parallel computing to have a test, e.g., by starting matlabpool(1)?

Best,

Chao-Gan

 

Hi,

 

Windows 7.

I turned parallel computing off and it didn't work either. But I think I know what the problem is. After canceling (control+c) the conversion , the files which were being converted were still in T1Raw or FunRaw folder. After deleting those files, it kind of works. With "kind of works" I mean, that it seems to convert all the files correctly, but sometimes it just doesn't convert all the files e.g. only 80 from 81. Not sure what the problem is, but I will try to find out and update this thread when I have some new information. 

Any ideas what the problem could be still appreaciated :).

 

greetings

 

David

 

YAN Chao-Gan

Wed, 01/13/2016 - 09:09

Permalink

Thanks, David!

Probably trying on another compute may give some hints.

Best,

Chao-Gan

it seems the conversion is succesful, but it doesn't seem to copy all the data from e.g. FunRaw, T1Raw to FunImg, T1Img. For example it converts all the T1 dicoms to nii.gz files, but it somehow gets stuck when copying the converted data to the T1Img folders and the nii.gz files stay in the T1Raw folder. Same with the FunRaw files. 

 Using a different computer doesn't change it, but I'm not sure if this is a DPABI problem or a problem from the dcm2nii tool. 

EDIT: This error seems to go away after restarting Matlab. It also seems to be when when first converting FunRaw's and then T1Raws but not when clicking both options at once in DPARSF. 

Maybe this is somehow helpful for diagnoses and bugfixes :)

Forums
DPABI/DPABISurf/DPARSF